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Cytoscape User Manual

1. Legent BC Key Aeibites UniProt 4 EntrezGene amp HGNC Official Symb Other Aliases 100 QOYNAS HERV Kic 19 HERV K_19q12 provirus ancestral 10054 OQov674 26236 20953 C orfs4 Protein HOCG 1 Uncharacterized pr 10059 EERTE 26238 21235 C6orflss Protein C orfl 3 chramosome G 10127 _ za aava 23643 17156 LY OG MO protemiLymphocyte antige 10174 QIYEYE 11196 L701 SEC 2 SIF pl2S PLFS EC2 3 interacting pra ae QIYGYI 23261 LEROG CAMTAL Calmodulin binding transonption 1020 OVvexd 28RD 23573 MORE MORC family CW type zine finger 10236 O9V6Xs 228s 18513 PHN MAW S4 Alpha fetoprotein regulada 10248 1076 Rey natched 1 First 100 emries are loaded for preview File Size 2972 Kiyes ial Cyloscape Deskiop New Session File Eda View elect Layo Flugins Help amp a Qaa g Bk i Control Panel R Network VizMapper Filters es Edges ae rogat BHIF3 664 E4 012983 SuMG2 6613 11125 Po1I9S6 5513 HEMT MGCLITIS1 STF h TUGI Lani E Lilia Poses 5512 SMT homolog 1 SHTI suppr suns arsed 15513 QAHTEA 54754 FLJ 1080 MOC104324 MY TGTA gidi ii oases ada SOT SOTA Veu binding prot TGE Gdade ii ood141 6446 SOK SGEIL Serine inreonine BLMH 642 105 MEEST Node Aibribute Browser Edge attribute Browser j Network Atribute Browser j Wekome to Cyioscape 2 5 Right tick drag to ZOOM Michdie clitk drag FAN At this
2. By default the Visual Style labeled default will be automatically applied to your network This default style has a purple background circular pink nodes and blue edges see sample screenshot below 53 Cytoscape User Manual o ramami TECIE ee 7 ____ J eer a Gere ee Dl ae TE e ihi r in Pa Step 2 Switch between different Visual Styles You can change visual styles by making a selection from the Current Visual Style dropdown list found at the top of the VizMapper Main Panel For example if you select Sample1 a new visual style will be applied to your network and you will see a white background and round blue nodes Additionally if you zoom in closer you can see that protein DNA interactions specified with the label pd are drawn with dashed red edges whereas protein protein interactions specified with the label pp are drawn with a solid light blue edge see sample screenshot below 54 Cytoscape User Manual o rewsumtyhie B m p i e a i a h i Leelee Per i jep tee fa ye Pig ia ma ee eee ees CI eee ET H E g rears Li aes aie er ee L j id a er ee Ln A I agg Hb LE Lr ir Oper beer dee m bir ec eee eres fete errre ma u m r m ji al p Sm oe es Se er ae Finally if you select Sample2 gene expression values for each node will be colored along a color gradient between red and green where red represents a low expressi
3. 2 Default Appearance Editor 52 Cytoscape User Manual AOPA Default Appearence for Sample3 R NODE_FILL_COLOR l NODE_BORDER_COLOR NODE_SHAPE 45 0 NODESIZE Node Edge Global W Lock Node With Height Apply e Clicking on the section labelled Defaults on the Main Panel will bring up this editor which allows users to visually edit the default appearance of nodes and edges for the selected visual style 3 Continuous Editors e These are editors for continuous mapping which is a mapping from numerical value to visual attributes They are accessed through the Visual Mapping Browser on the Main Panel Using these windows users can edit continuous mapping more intuitively e Color Gradient Editor e Continuous to Discrete Editor e Continuous to Continuous Editor These editors will be discussed in further detail below Introduction to Visual Styles The Cytoscape distribution includes several predefined visual styles to get you started To demonstrate these styles try out the following example Step 1 Load some sample data e Load a sample network From the main menu select File gt Import Network Multiple file types and select sampleData galFiltered sif e Layout the network select Layout gt yFiles Organic e Load a sample set of expression data From the main menu select File gt Import Attribute Expression Matrix and select sampleData galExpData pvals
4. Cytoscape User Manual Table of Contents Cyloscape 2 al User Mamia eenen eE EE ERER rE na Wedane EE oraa i 2 IMGT OIG E a EA E E A E EE A AE A E E E A E E A E 3 Descon aie gece ree E EE E E E 3 ETE SS E E T E EEEE E T E E E A E E T E ES 3 WEEN e 9 EE E EE E E E EE A E 4 Lavandin C y OSC ae derrr r E E 5 Syse regure MeN sereen i i E E TE TEA 5 Geine Sre d eenen E EEEE E E E E E 5 ek TOUT OR OC e eS E E E E E E E E EREE 8 Toe MEMS esc a suai pad ocscn enact aaecetes nes eaten oe atone tae agama ant aaceeansaaeeanecenes 10 Network IVIAMASCINONE errien keri EAE aean TEE reia eSEE n 12 The INetwotk Overview WiIMdOW scicsst cscnadetecusesrscnavarusiasnaciacsenabulecsnaaesetenenesicieewuastanedulace 13 Command Line Ars UMM ic cncasucecsc ss cia renen rR AEE EAE E Er EEES EE Eta 14 C ytoscape Prei rences siesinor ansen r E EE 16 Mama Simi PROPETUIES 25c40 ctcsnconeieswscsestancos iT ENE TEE iR TEE 16 Manac ing BOOkMaArKS serrsrgerr inbe eT r rE E E ETE 17 Manasins Proxy Servers serret REEE REE EEE E E EE ESERE 17 ire aul INCE WON oS te ape ocara ects E E E 18 Import Fixed Format Network Files cccccecece nce ee eee e ence eee e E Ea akenda Taitea 18 Inport Pree Formiat Mable Piles scicaccscathesssdaacestscsanedusscenaaeeetanetendgcmceusoteredubecanenesemiveounients 19 Edita New INCL WOK pan caceesecenuavtandsaccisoes actin AEE E E EEEE AEREE 23 Supported Network File TOrnmmalS sscosresenre dirine ns EE EE EEEE noone 23 SE FOC een E E
5. gt NP_054861 np np s np np tester ipiToNPHash tester bioproc open bioproc txt w molfunc open molfunc txt w cellcomp open cellcomp txt w bioproc write species np np s type Biological Process curator GO n np np species molfunc write species np np s type Molecular Function curator GO n np np species cellcomp write species np np s type Cellular Component curator G0 n np np species lines open associationFilename read split n sys stderr write found np np d lines n np np len lines Q i for line in lines if line find 0 or len line lt 2 continue tokens line split t goOntology tokens 8 goIDraw tokens 4 goID goIDraw split 1 ipiName fixCanonicalName tokens 10 if len ipiName lt 1 continue if not ipiToNPHash has_key ipiName continue refseqName ipiToNPHash ipiName printName refseqName printName ipiName if ipiName tester print np np s np np s has go term np np s np np tester printName golID if goOntology C cellcomp write np np s np np s n np np printName goID elif goOntology P bioproc write np np s np np s n np np printName goID elif goOntology F 111 Cytoscape User Manual molfunc write np np s np np s n np np printN
6. Edit default values Open the Default Appearance Editor by clicking on the Defaults graphics window shown below in the VizMapper Main Panel 61 Cytoscape User Manual BnB Default Appearence for Tutorial WL KODE Fl COLCA Nene scapes couor soom 35 0 noorse HDE LABEL Font NDE PONT FALE Wf Lorik Mode With height Apply Diode Edge Gishal Step 5 Change the default node shape To set the default node shape to triangles click Node Shape in the Default Visual Properties list A list of available node shapes will be shown Click on the Triangle icon and then click the Apply button The Default Appearance Editor will be automatically updated You can edit other default values by clicking on visual attribute names on the list In the example shown below the node shape is set to Triangle while the node color is set to blue 6 6 Default Appearence for Tutorial WL BODE Fl COLCA ee ee a HOOF SHA Lad ly oo RODE SEE BODE LAREI Font BDO PONT FAZE Mf Lork Mode With height as hede Edge Giahal Step 6 Apply your settings When you finish editing click the Apply button at the bottom of the editor Your new Visual Style will be applied to the current network as shown below 62 Cytoscape User Manual Edge Label Opacity Doune Lick ip cre e AAA Cytoscage Desktop New esgan G oe T SH aA9Q0 88 BH i Contra Pane d AAA galFijtered sif T Network Wighlapoer Edi
7. Install Cytoscape There are a number of options for downloading and installing Cytoscape All options can be downloaded from the http cytoscape org website e Automatic installation packages exist for Windows Mac OS X and Linux platforms e You can install Cytoscape from a compressed archive distribution e You can build Cytoscape from the source code e You can check out the latest and greatest software from our Subversion repository Cytoscape installations regardless of platform containing the following files and directories Cytoscape User Manual Table 3 library jar files needed to run Cytoscape Directory containing cytoscape plugins in jar format C galExpData pvals Sample gene expression matrix file galFiltered nodeAttrTable xls Sample node attribute file in Microsoft Excel format galFiltered cys Sample session file created from datasets above plus GO Annotations galFiltered sif Identical network in Simple Interaction Format BINDyeast sif Network of all yeast protein protein interactions in the BIND database as of Dec 2006 BINDhuman sif Network of all human protein protein interactions in the BIND database as of Dec 2006 yeastHighQuality sif Sample molecular interaction network file interactome_merged networkTable gz Human interactome network file in tab de limited format From Ideker et al Science 292 929 2001 Obtained from data hosted at http
8. These are nomal networks that can be loaded into Cytoscape The annotation bookmarks are URLs pointing to ontology annotation files The annotation bookmarks are only used when importing an ontology Managing Proxy Servers You can define and configure a proxy server for Cytoscape by going to Edit Preferences Proxies 17 Cytoscape User Manual amp Proxy server setting Type Host name DIRECT After the proxy server is set all network traffic related to loading a network from URL will pass through the proxy server Other plugins use this capability as well Creating Networks There are 3 different ways of creating networks in Cytoscape 1 Importing pre existing formatted network files 2 Importing pre existing unformatted text or Excel files 3 Creating an empty network and manually adding nodes and edges Import Fixed Format Network Files Network files can be specified in any of the formats described in the Supported Network Formats chapter Networks are imported into Cytoscape through the Import Network window which can be accessed by going to File gt Import Network multiple file types The network file can either be located directly on the local computer or found on a remote computer in which case it will be referenced with a URL Load Networks from Local Computer By default Cytoscape loads networks from the local computer The Import Networks dialog shows a default setting of Data S
9. http www geneontology org GO current annotations shtml OBO File An OBO file is the ontology DAG itself This file defines the relationships between ontology terms Cytoscape 2 4 and onwards can load all ontology files written in OBO format The full listing of ontology files are available from the Open Biomedical Ontologies OBO website e OBO Ontology Browser http obo sourceforge net browse html Sample OBO File gene_ontology obo http www geneontology org ontology gene_ontology_edit obo format version 1 2 date 27 11 2006 17 12 saved by midori auto generated by OBO Edit 1 002 94 Cytoscape User Manual subsetdef goslim_generic Generic GO slim subsetdef goslim_goa GOA and proteome slim subsetdef goslim_plant Plant GO slim subsetdef goslim_yeast Yeast GO slim subsetdef gosubset_prok Prokaryotic GO subset default namespace gene_ontology remark cvs version Revision 5 49 Term id GO 0000001 name mitochondrion inheritance namespace biological_process def The distribution of mitochondria including the mitochondrial genome into daughter cells after mitosis or meiosis mediated by interactions between mitochondria and the cytoskeleton GOC m synonym mitochondrial inheritance EXACT is_a GO 0048308 organelle inheritance is_a GO 0048311 mitochondrion distribution Term id GO 0000002 name mitochondrial genome maintenance namespace biological_process def The mai
10. 1 oalollolo The edge attribute that contains the weights Manual Layout The simplest method to manually organize a network is to click on a node and drag it If you select multiple nodes all of the selected nodes will be moved together 39 Cytoscape User Manual Rotate CytoPanel 5 al Rotate in Degrees 0 90 180 270 360 L Rotate Selected Node Selecting the Layout Rotate option will open the Rotate window in CytoPanel 5 This function will either rotate the entire network or a selected portion of the network The image below shows a network with selected nodes rotated Before AAA sample e CytoPanel 5 ia romte Seale P Rotate in Degrees 0 90 180 270 360 v Rotate Selected Node ii After AAA sample e CytoPanel 5 ia Goe Seale gt Rotate in Degrees 0 90 180 270 360 Vv Rotate Selected Node Mi 40 Cytoscape User Manual Scale CytoPanel 5 Fal Rotate b Scale Y a a 1 8 1 4 1 2 1 2 4 8 l l Scale Selected Nodes Only Selecting the Layout Scale option will open the Scale window in CytoPanel 5 This function will scale the position of the entire network or of the selected portion of the network Note that only the position of the nodes will be scaled not the node sizes Node size can be adjusted using the VizMapper The image below shows selected nodes scaled Before ef A sample AOA Cyt
11. 2 Step 9 Define the colors between points Double click on the leftmost triangle facing left and a color palette will appear Choose a shade of yellow and click OK Leave the triangle at 1 white Double click on the triangle set at 2 and set its color to red Set the rightmost triangle to black e080 Gradient Editor for Node Color Continuous Mapping for Node Color lt V Th 2 0000 Min 2 426 gallRGexp Max 2 058 Range Setting 2 a Add Delete The color gradients will immediately appear in the network window All nodes with a gall RGexp value less than 1 will be set to yellow and all nodes with a gall RGExp value greater than 2 will be black Ad ditionally all values between 1 and 2 will be painted with a white red color gradient A sample screenshot is below 66 Cytoscape User Manual rami riie E A i ie be Se CE oe Eple y ppe Tep i ip l ee a Di a le a age G h g aH a a A l li Car I e i Tn l J Sa nme D Tutorial 4 How to Use Utilities for Discrete Mappers The following tutorial demonstrates new features in Cytoscape 2 5 The new VizMapper user interface has some utilities to help users editing discrete mappings The goal of this section is learning how to set and adjust values for discrete mappings automatically 1 Load a sample network From the main menu select File gt Import Network and select sampleData galFiltered s
12. Additionally database identifiers from every database where the gene is stored may be used to refer to a gene e g protein accession numbers from Swiss Prot If one data source uses the formal name while a different data source used a common name or identifier then Cytoscape must figure out that these two different names really refer to the same biological entity Cytoscape has two strategies for dealing with this naming issue one simple and one more complex The simple strategy is to assume that every data source uses the same set of names for every object If this is the case then Cytoscape can easily connect all of the different data sources To handle data sources with different sets of names as is usually the case when manually integrating gene information from different sources Cytoscape needs a data server that provides synonym information see the chapter on Annotation A synonym table gives a canonical name for each object in a given organism and one or more recognized synonyms for that object Note that the synonym table itself defines which set of names are the canonical names For example in budding yeast the ORF names are commonly used as the canonical names 26 Cytoscape User Manual If a synonym server is available then by default Cytoscape will convert every name that appears in a data file to the associated canonical name Unrecognized names will not be changed This conversion of names to acommon set allows Cytoscape
13. Atinbuies wv Column 1 a PPI Ontology node A Pp node 2 node_1 pp node_2 M0445 amp node_2 pp node_3 nocde_F pp nocde_l MEDDA node 3 pp node_1 nocde_ pp node_34 MEOS46 Key Matched J First 100 entries are loaded for previews File Size B1 Bytes Import Cancel The basic operation of the Ontology and Annotation Import function is the same as that of the Attribute Table Import The main difference is that you need to specify an additional key for mapping parece a beter File to Ontology Mapping Key Column in Annotation File Ontology lt olumn2 amp Protein protein interaction By selecting a column from the Key Column in Annotation File dropdown list you can specify the key for mapping between ontology terms and the annotation file e Note When you load Gene Association files Cytoscape uses a special loader program designed only for Gene Association files Because of this program all attributes will be named automatically Also ontology IDs will be converted into term names and NCBI taxonomy ID will be converted into actual species name However for custom annotation files those processes will not be applied All ontology terms will be mapped as term IDs Linkout LinkOut provides a mechanism to link nodes and edges to external web resources within Cytoscape Right clicking on a node or edge in Cytoscape view opens a popup menu with a list of web links 104 Cytoscape User Manual The externa
14. E A tac E EAA T E E EE EAE E 24 OME Foma 4 cienenzechaxadien escent EEE A EAER E E E 25 PIV UN Whe A OTTAT AG sherri des tare do esr hata E earnestness coder E E ARE E E EE A 25 SBML Systems Biology Markup Language Format cceccecec ence eee ee eee eeeeeeneeeeneenen ZS BioPAX Biological PAthways eXchange Format cccccececceceeeeceeeee ences eneeaeeseneeaeneeas 25 PSEML FONOJ cerisa EEEE EEEE spac imenksorinedatadaieues 26 Delimited Text Table and Excel Workbook 0 c cece ccc cc ese nc ence cee ene eens ene eaenseaenseneeaenneas 26 Node Naming Issues im ylOSCADG sce xcnicrccacseriuececiotsnaniwarexerrssecueniuerereaucecsnaneaeteeeasace 26 Node and Se Ai DUE Siac teccceenedacichonceantteesuekdan con a a ia a na kia al Cyloscape AtimbUe FIG FORMAL siicssesdsenssdccueneiesenatenddemoansedsmenehicawonnsetunetehecunceesetivemhicers 2l Import Attribute Table Files ss cccrererereipeieirerre ekg ien ER KRESE r EEE EE 29 Loading Gene Expression Attribute Matrix Data 00 cece cece ecec eee ee eee eeeeeeeeseneeaeeseaeeaenneas 33 Data Fee MPA soca cena E since aiecstist E E E EEE EEEE 33 General PLOCCUULe ax2ticacnsaccecsseranepunccasonmseaarependcxcesnaesemetulecusaensesanedinaccnentaeeunadenaceuensceea 34 WV Od EX ANC eere E E aecsnwenechsmasanehoncesandenn E 34 Detailed file format Advanced users a5 csscaascsiwnvecsstacass sonnesevauvadassaniverixenisaiasntiasexaoweonines 35 IN ey Oa and Layou eesis
15. P3399 7040 7040 TGFB1 TGFBL P01137 P01137 nmr nuclear magnetic resonance Currently not available 8679613 Homo sapiens Homo sapiens protein protein BIND 2 TGFB1 TGFB1 72085 This data file 1s a tab delimited text and contains network data interactions edge attributes and node at tributes To import network and edge attributes from this table you need to choose Unique ID A as source Unique ID B as target and Interactor types as interaction type Then you need to turn off columns used for node attributes Alternative ID A species B etc Other columns can be imported as edge attributes The network import function cannot import node attributes only edge attributes To import node attributes from this table please see the Attributes section of this manual Note 1 This data is taken from the A merged human interactome datasets by Andrew Garrow Yeyeyjide Adeleye and Guy Warner Unilever Safety and Environmental Assurance Center 12 October 2006 Ac tual data files are available at http www cytoscape orghttp cytoscape org cgi bin moin cgi Data_Sets Basic Operations To import network text Excel tables please follow these steps 1 Select File Import gt Network from Table Text MS Excel 2 Select a table file by clicking on the Select File button 3 Define the interaction parameters by specifying which columns of data contain the Source Interaction Target Interaction and Interaction Type Setting the Interaction
16. class Again the class will be inferred if it 1s not specified in the header line Lists are not supported by the visual mapper and so can t be mapped to visual attributes Newline Feature Sometimes it is desirable to for attributes to include linebreaks such as node labels that extend over two lines You can acomplish by inserting into the attribute value For example newlineAttr YJL157C This is a long nline for a label Import Attribute Table Files As of Cytoscape 2 4 importing delimited text and MS Excel attribute data tables is now supported Using this functionality users can now easily import data that isn t formatted into Cytoscape node or edge attribute file formats as described above 29 Cytoscape User Manual MET ANMAT ee import Attribute from Table Data Sources Amibe s Hode gt Edge Hetaork input File file cellar iageriskone workipace fododcape build sfcybadcape v2 4 0 b1 jgimpihDma gi Espira pale Calect File Aai eil x Show Advanced Happing Opiions a Show Text File Import Options Annotation File to Anm ibute Happi Key Cohumn in Annotation File Key Attribute for Network Prim my Eyy Sy CEHE Alies Column tribute Mame Daa Type bh dinani ame GENE Jg String l CE COMMON Ih iring gallik dh String gali LE Float galeih Ky Float Text nle Import Options Delimiter Preview prionsa w Tab _ Comma _ Semicolom of Space _ Ciher Show all eniries inthe file E Showin 100 gt encrie
17. each protein is identified by its NP RefSeq number These two naming systems IPI and RefSeq are two of many that you can use to define canonical names when you run Cytoscape For budding yeast it is much easier the yeast community always uses standard ORF names and so Cytoscape uses these as canonical names For human proteins and genes there is no single standard The solution for those working with human genes or proteins is once you have downloaded the annotations file to 1 Decide which naming system you want to use 2 Download ftp ftp ebi ac uk pub databases GO goa HUMAN xrefs goa This cross reference file when used strategically allows you to create Cytoscape compatible annotation files in which the canonical name is the one most meaningful to you 3 Examine xrefs goa to figure out which column contains the names you wish to use 4 Make a very slight modification to the python script described below and then 5 Run that script supplying both xrefs goa and that annotation file as arguments Here are a few sample lines from xrefs goa SP 000115 IPI00010348 ENSP 00000222219 NP_001366 BAA28623 AAC77366 AAC35751 AAC39852 BAB55598 AAB51172 AAH10419 2960 DNASE2 SP 000116 IPI00010349 ENSP00000324567 ENSP00000264167 NP_003650 CAA70591 327 AGPS SP 000124 IPI00010353 ENSP00000265616 ENSP00000322580 NP_005662 BAA18958 BAA18959 AAH20694 Note that line wrapping has occurred here each line in th
18. example you can e Specify a default color and shape for all nodes 44 Cytoscape User Manual T Deui Apooaronce for dati Default irual Proper NODE ALL COLOR HODE ORDER CHLIR Hode hapa lt gt Di amom Tniangla aE ai Ellipse ot Knacks Made Wih Me igha e Encode specific physical entities as different node shapes 45 Cytoscape User Manual D arnirio acid oxidase _ dino 2 oxomentanoa B Ornithine gt e Set node sizes based on the degree of connectivity of the nodes You can visually see the hub of a net work 46 Cytoscape User Manual e or set the font size of the node labels instead 47 Cytoscape User Manual e Set node widths and heights based on label size 48 Cytoscape User Manual eS a pasa EA FLO ET EE TTE ETTEI TLL DEN re ee A ade i ike Bie ee ed ee Bie ee ee Pe SE er he Pal ie ee oe H a O RhE Ae a p a m El pien af m e oal ee Be E a Mi Rj NTE l A LE uretara n pra pee a cL a CEEE i GILL ELi LELIT Sedim ii IF i Gehi viner ee eee E ALN Ti E HFH ee ose EELE H J A Hit el i i p rE nn ee n ee ed eg ee ae eB ee ea teu Pe BR pede Eb pee er a Pere BLE mi Fi Ape a rb se PEN Fee igri amp Po Le G S L LCI eed pee ere ees Se iE pode raaa i po eg T Ail r igh De Dy pedir eq eld mad qlee eg r pee ee ee ee Pee pe myg OO M ee CI N benim si a ii el oe R S a
19. for the new filter E Create new filter T Delete filter Rename filter e Copy existing filter 80 Cytoscape User Manual New Filter name My First Filter 2 Define the filter After a new filter is created the filter definition is initially empty Filters can be defined by choosing attrib utes one at a time in the attribute dropdown list and clicking the Add button which will add a widget for defining the desired attribute criteria Note that each attribute has a prefix either node or edge denoting what type of attribute it is Text based or String attributes will display a widget listing all available values while numeric attributes will display a range slider both are shown below F4 Control Panel fe Network VizMapper Editor Filters Current Filter session My First Filter Filter Definition Attribute node gallRGsig Advanced annotation Date O000 Aa For each widget the name of the attribute it represents is on the left and there is a trash can icon on the right Clicking on the trash can icon will delete the widget In this way the filter definition can be modified after it is defined 3 Apply the filter Now that a filter is defined you can enter appropriate values string patterns for text or value ranges for numbers and click the Apply button to select nodes edges from your network The search values for Nodes and edges are selected using text and nu
20. has a feature that allows users to override visualizations created by the VizMapper for individual nodes and edges This feature is available by right clicking on a node or edge and then clicking on the Visual Mapping Bypass menu bi aa 7 ail vha Pa T Mapping Bypass oe Node Visualization 0 Fill Color Reset Fill Color Border Color Border Line Type v Size LI Reset Size Shape Reset Shape Label Label Color LI Label Position Font Font Size L Reset All Each visual property of the node or edge is displayed When a property is overridden a checkmark appears next to the property and a Reset lt Property Name gt menu option appears directly below it By clicking this Reset option the bypass will be removed and the attribute will be displayed as defined by the VizMapper At the bottom of the menu a Reset All option appears When clicked this will remove all by passes for the specified node or edge In the example above you can see the the selected node size color and shape have been overridden This is apparent in the appearance of the node itself and by the check marks in the popup menu It is important to realize that the the Visual Mapping Bypass only works for individual nodes and edges and not for all nodes or edges of a specific type Using the bypass function is not particularly resource in tensive meaning you can use it as much as you like However if you ever find yourself
21. identical nodes The name of each node will be the name in this file by default unless another string 1s mapped to display on the node using the visual mapper This is discussed in the section on visual styles The name of each edge will be formed from the name of the source and target nodes plus the interaction type for example sourceName edgeType targetName The tag lt relationship type gt can be any string Whole words or concatenated words may be used to define types of relationships e g geneFusion cogInference pullsDown activates degrades inactivates inhibits phosphorylates upRegulates etc Some common interaction types used in the Systems Biology community are as follows e AE E protein protein interaction Ge AA A protein gt DNA e g transcription factor binding upstream of a regulating gene Some less common interaction types used are 24 Cytoscape User Manual EE E OEE protein gt reaction EC EEEE T reaction gt compound OT AEE compound gt reaction P Lota ea Oa genetic lethal relationship EEE OE TAT protein metabolite interaction O E E EOT metabolite protein interaction Delimiters Whitespace space or tab is used to delimit the names in the simple interaction file format However in some cases spaces are desired in a node name or edge type The standard is that 1f the file contains any tab characters then tabs are used to delimit the fields and spaces are considered part of the name If t
22. libraries e The Colt Distribution Open Source Libraries for High Performance Scientific and Technical Computing in Java Information is available at http hoschek home cern ch hoschek colt e Graph INterface librarY a k a GINY Information is available at http csbi sourceforge net e JDOM Information is available at http www jdom org e JUnit Information is available at http junit org e JGoodies Looks Information is available at http www jgoodies com freeware looks index html e Piccolo Information is available at http www cs umd edu hcil jazz e Type Specific Collections Library from Sosnoski Software Solutions Inc Information is available at http www sosnoski com opensrc tclib e Xerces Java XML parser Information is available at http xml apache org xerces e CLI command line parser Information is available at http jakarta apache org commons cli e FreeHEP library Information is available at http java freehep org This product includes software developed by the Apache Software Foundation http www apache org This product includes software developed by the JOOM Project http www jdom org One step installation of the Cytoscape software is accomplished using the nstallAnywhere product from ZeroG Software Inc http zerog com Appendix A Old Annotation Server Format Handlers for the following format still exist in Cytoscape as legacy code however we strongly recommend usin
23. licensed at no charge to all third parties under the terms of this License d If a facility in the modified Library refers to a function or a table of data to be supplied by an application program that uses the facility other than as an argument passed when the facility is invoked then you must make a good faith effort to ensure that in the event an application does not supply such function or table the facility still operates and performs whatever part of its purpose remains meaningful For example a function in a library to compute square roots has a purpose that is entirely well defined independent of the application Therefore Subsection 2d requires that any application supplied function or table used by this function must be optional if the application does not supply it the square root function must still compute Square roots These requirements apply to the modified work as a whole If identifiable sections of that work are not derived from the Library and can be reasonably considered independent and separate works in themselves then this License and its terms do not apply to those sections when you distribute them as separate works But when you distribute the same sections as part of a whole which is a work based on the Library the distribution of the whole must be on the terms of this License whose permissions for other licensees extend to the entire whole and thus to each and every part regardless of who wrote it Thus it
24. membrane bound organelle Annotation Data 102 Cytoscape User Manual 1731YAP1802 G0 0006897 scD REF ISS YGR241C 7 HP 101 YAP3 G0 0005634 5GD_REF IPI c YHLoosc 101 YAP3 GO 0003700 SGD_REF DA F YHLoosc 101 YAP3 G0 0006357 5GD_REF IDA P YHLoosc _ is7 YAPS_ _ GO 0005634 sco REF IC GiC_bZIP basi YIROISW 157 YAPS GO 0003702 SGD_REF IDA F bZIP basil YIROIW 157 YAPS GO 0000083 SGD_REF IPI P bZIP basqYIROIBW 157 YAPS GO 0045944 SGD_REF IDA P bZIP basqYIROIBW Mapping Result annotation GO CELLULAR_COMPONENT YIROLBW nucleus 5000001457 YAF5 transcription factor If you want to map ontology terms onto network objects you need to create a custom annotation file The annotation file should contain at least 2 columns a primary key and an ontology term ID The primary key is the value used for mapping between the annotation file and network Usually the node edge ID is used as the primary key but you may choose any of the available attributes The Ontology term ID is the key used for mapping between the annotation file and the ontology DAG Using these data sources you can annotate network objects in Cytoscape Suppose you have a small network node_1 pp node_2 node_3 pp node_1 node_2 pp node_3 and you want to annotate this network with Ontology A which is an ontology DAG available in OBO format In this case you need an annotation table file that looks like this node_1 0A 0000232 nod
25. names Unzip the archive 2 Load sample network file Open network import dialog from File gt Import gt Network multiple file types Then click URL radio button and import Human Protein Protein Rual et al Subnetwork for tutorial 3 Open attribute table import dialog from File gt Import gt Attribute from Table 4 Select human dic_cyto txt as the input file 5 Check Show Text File Import Options and click Transfer first line as attribute names checkbox lt listitem gt Uncheck Show Text File Import Options and check Mapping Options lt listitem gt 6 Select EntrezGene as Primary Key 7 Right click on EntrezGene column name and set the type to String 8 Do the same for HGNC 9 Right click on Other Aliases and select List as the data type 10 Check Other Aliases as Alias under Alias checkboxes 11 Now the Table Import dialog looks like the following screenshot 98 Cytoscape User Manual Import Annotation File l zi Import Attribute from Table Bada Sources Anuibutes Hode Edge Nereork Input File file cellarfusers kono workspace NameMappingrier arser OnpinalData hurvan dic cyto tan Ahvaonomel w Show Manin Opies _ Show Tew File knpom Opens Annctation File io Adtribute Mapping Key Column in Annotation File Key Atuibute for Network Primary Kev Sip ErmrexGene a alas Column ganritute Name Uri rot iy String O EntrerGene O Hone Diiia Sembol i ther Aliases
26. of this License Also you must do one of these things a Accompany the work with the complete corresponding machine readable source code for the Library including whatever changes were used in the work which must be distributed under Sections 1 and 2 above and if the work is an executable linked with the Library with the complete machine readable work that uses the Library as object code and or source code so that the user can modify the Library and then relink to produce a modified executable containing the modified Library It is understood that the user who changes the contents of definitions files in the Library will not necessarily be able to recompile the application to use the modified definitions b Use a suitable shared library mechanism for linking with the Library A suitable mechanism is one that 1 uses at run time a copy of the library already present on the user s computer system rather than copying library functions into the executable and 2 will operate properly with a modified version of the library if the user installs one as long as the modified version is interface compatible with the version that the work was made with c Accompany the work with a written offer valid for at least three years to give the same user the mater ials specified in Subsection 6a above for a charge no more than the cost of performing this distribution d If distribution of the work is made by offering access to copy from a desig
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28. repeating the same bypasses then you should consider using the VizMapper instead Bypass is accomplished using special attributes with names like node fillColor and node shape These are normal Cytoscape attributes and can be seen and edited in the Attribute Browser The value of the attribute is a String representation of a property For example color is represented by 3 integers representing the RGB red green blue value of the color Different types of properties have different string representations When in doubt just use the right click menu to create valid attribute values 75 Cytoscape User Manual Because bypass values are specified using normal attributes these attributes will persist between sessions only as long as you save your session If you don t save your session you will lose whatever bypass values you set Finding and Filtering Nodes and Edges QuickFind Cytoscape includes a Quick Find feature which enables you to quickly find nodes and edges File Edit View Select Layout Plugins Help Za AQAA DAut B Search for Configure matching nodes Quick Find edges Using Quick Find is very simple Here is how it works e Import a network For example load up sampleData galFiltered sif e Start typing in the text box For example enter yd The search box will automatically display a list of all matching nodes ydorsw Us ydl013w yolOl4w yalO23c Searcn yalO3s0w yal063c e Select a matc
29. run Cytoscape from any location you want Quick Tour of Cytoscape When a network is loaded Cytoscape will look something like the image below i Cytoscape Version 2 5 File Edit View Select Layout Plugins Help aoe Cytoscape Desktop New Session jeoGQAQgag agin B Control Pare 4 eaea galFiltered sif T Network VizMapper Editor P i Ketao Nodes Edges 3310 3620 Data Panel H canna Node Attribute Browser Edge Attribute Browser Network Attribute Browser Welcome to Cytorcape 2 5 Right click drag to ZUOM Middle clitk drag to FAN The main window here has several components e The menu bar at the top see below for more information about each menu e The toolbar which contains icons for commonly used functions These functions are also available via the menus Hover the mouse pointer over an icon and wait momentarily for a description to appear as a tooltip e The network management panel top left panel This contains an optional network overview pane shown at the bottom left Cytoscape User Manual e The main network view window which displays the network e The attribute browser panel bottom panel which displays attributes of selected nodes and edges and enables you to modify the values of attributes The network management and attribute browser panels are dockable tabbed panels known as CytoPanels You can undock any of these panels by clicking on the Float Window control a a in the up
30. selected filters Select All Filter Select All Filter Node canonicalName YL Node canonicalName YL Node canonicalName C Node canonicalName C Node canonicalName Node canonicalName Node null 0 0 Node null 0 0 NodeTopology NodeTopology BooleanMeta BooleanMeta Apply selected filter _ Negate The Boolean Meta Filter allows you to define a new filter that is a logical combination of existing filters Available filters are displayed By selecting one or more filters you can then choose whether Nodes or Edges pass ALL AND AT LEAST ONE OR or ONLY ONE XOR of the selected filters Once created Boolean filters can then themselves be combined using the Boolean filter to create arbitrarily complex logical combinations of filters Note that unlike the String and Numerical Filters Boolean filters will need to be assigned a name manually Saving Filters Filters are currently saved automatically in the filters props file found in the cytoscape directory found in each user s home directory Once created filters are saved for future sessions as long as you exit Cyto scape normally via File gt Quit i e not via ctrl c on Linux Running filters Any available filter can be run by pressing the Apply selected filter button When a filter is applied to your network and multiple nodes or edges are selected all of the normal selection related operations may be performed su
31. software patents pose a constant threat to the existence of any free program We wish to make sure that a company cannot effectively restrict the users of a free program by obtaining a restrictive license from a patent holder Therefore we insist that any patent license obtained for a version of the library must be consistent with the full freedom of use specified in this license Most GNU software including some libraries is covered by the ordinary GNU General Public License This license the GNU Lesser General Public License applies to certain designated libraries and is quite 112 Cytoscape User Manual different from the ordinary General Public License We use this license for certain libraries in order to permit linking those libraries into non free programs When a program is linked with a library whether statically or using a shared library the combination of the two is legally speaking a combined work a derivative of the original library The ordinary General Public License therefore permits such linking only if the entire combination fits its criteria of freedom The Lesser General Public License permits more lax criteria for linking other code with the library We call this license the Lesser General Public License because it does Less to protect the user s freedom than the ordinary General Public License It also provides other free software developers Less of an advantage over competing non free programs These disadvantages are
32. some default values Step 1 Load a sample network From the main menu select File Import gt Network Multiple file types and select sampleData galFiltered sif Step 2 Open the VizMapper Select the View Open VizMapper menu option or select the VizMapper icon in the main button bar or click on the VizMapper tab in the Control Panel at the left of the screen You will now see a VizMapper Main Panel as shown below m aF Te Network Editor La Current Visual Style default He Fa Defaults Visual Mapping Browser i E F Node Visual Map E Node Label ID F Unused Properties Node Color Node Border Color Node Shape Node Sore Node Width Node Height Node Font Face Node Font Sire Node Label Color T 60 Cytoscape User Manual J Create a new visual style Click the Options button and select Create new visual style Then enter a name for your new visual style when prompted You will see an empty visual style in the VizMapper Main Panel as shown below fe Network Current Visual Style Tutorial VS1 B Defaults Visual Mapping Browser Y Unused Properties Node Color Double Click to cre Node Border Color Double Click to cre Kinda Ghana Meikle liel tea rro Since no mapping is set up yet all visual attributes are listed in the Unused Properties category From this panel you can create node edge mappings for all visual properties Step 4
33. subject to these terms and conditions You may not impose any further restrictions on the recipients exercise of the rights granted herein You are not responsible for enforcing compliance by third parties with this License 11 If as a consequence of a court judgment or allegation of patent infringement or for any other reason not limited to patent issues conditions are imposed on you whether by court order agreement or other wise that contradict the conditions of this License they do not excuse you from the conditions of this Li cense If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations then as a consequence you may not distribute the Library at all For example if a patent license would not permit royalty free redistribution of the Library by all those who receive copies directly or indirectly through you then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Library If any portion of this section is held invalid or unen forceable under any particular circumstance the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims this section has the sole purpose of protecting the integrity of the free so
34. the reason we use the ordinary General Public License for many libraries However the Lesser license provides advantages in certain special circumstances For example on rare occasions there may be a special need to encourage the widest possible use of a certain library so that it becomes a de facto standard To achieve this non free programs must be allowed to use the library A more frequent case is that a free library does the same job as widely used non free libraries In this case there is little to gain by limiting the free library to free software only so we use the Lesser General Public License In other cases permission to use a particular library in non free programs enables a greater number of people to use a large body of free software For example permission to use the GNU C Library in non free programs enables many more people to use the whole GNU operating system as well as its variant the GNU Linux operating system Although the Lesser General Public License is Less protective of the users freedom it does ensure that the user of a program that is linked with the Library has the freedom and the wherewithal to run that program using a modified version of the Library The precise terms and conditions for copying distribution and modification follow Pay close attention to the difference between a work based on the library and a work that uses the library The former contains code derived from the library whereas the latter must b
35. 8 Cytoscape User Manual Select Layout Plugins Help m Rotate o Q s Scale Align and Distribute 1 yFiles Circular Minimize Edge Crossings for Selected Nodes XU Organic Cytoscape Layouts Hierarchic JGraph Layouts t Random Mirrorx Mirrory a Pee Several other alignment algorithms including a selection from the JGraph project http jgraph source forge net are also available under the Layout menu Layout Parameters Many layouts have adjustable parameters that are exposed through the Layouts Settings menu option This will pop up the following dialog which allows you to choose which layout algorithm settings to adjust The settings presented vary by algorithm and only those algorithms that allow access to their parameters will appear in the drop down menu at the top of the dialog Once you ve modified a parameter clicking the Execute Layout button will apply the layout This be repeated until a useful layout is achieved Settings can be saved using the Save Settings button Ef Layout Settings Layout Algorithm Force Directed Layout Force Directed Layout Settings Default Spring Coefficient Default Spring Length Default Node Mass Number of Iterations The minimum edge weight to consider The maximum edge weight to consider 86273157E308 Integration algorithm to use Only layout selected nodes as a T iT Wo 3 A cE E a E Mga fia aLI
36. B rol Parel Ei Comal Vaklagpe Ednor amp Ab erie Bere g Atti Breas betel AT bes Bede Weliorte to Cyfoscape 2 5 Right click daag ba Doo oe Note on Memory Consumption For users interested in loading large networks the amount of memory needed by Cytoscape will increase Memory usage depends on both number of network objects nodes edges and the number of attributes Here are some rough suggestions for memory allocation Suggested Memory Size Without View Table 4 Number of Objects nodes edges Suggested Memory Size 0 70 000 512M default 70 000 150 000 800M Suggested Memory Size With View Table 5 Number of Objects nodes edges Suggested Memory Size 0 20 000 512M default 20 000 70 000 800M Cytoscape User Manual To increase the maximum memory size for Cytoscape you can specify it from command line For example if you want to assign 1GB of memory type java XmxIGB jar cytoscape jar p plugins from the command line For more details see How to increase memory for Cytoscape Note on Directory Location For the application to work properly all files should be left in the directory in which they were unpacked The core Cytoscape application assumes this directory structure when looking for the various libraries needed to run the application If you are adventurous you can get creative with the CLASSPATH and or the cytoscape jar manifest file and
37. CEE NEEE E EEEE EEEE 105 PREKMOW EGC Meng ho sercacsoent nEn sense rasi ERE EE E AE E TEE EEE SEE 106 Appendix A Old Annotation Server Format cccccececceceeeeceeeee ences sees eeeenseeeeseaeeeeeseeenneees 106 Building your own annotation files lt s6 aci texasiecna ses Sedtanetiecesiassus bawcidadnteiindaweinacestaseentawede 106 Lead Data into CV LOSCADG 521s ccntenancnenaceccsnnacanesctetaneranenansenseees wanoaeandsntabanennnaencaeneeeaeents 108 Getting and Reformatting GO Data os cctssoosavacs contaneansaisacomucieniaesanbacnnialamianenitecseaianteose 108 ey COT seip Nec Scots ae recs an E 110 Appendix B GNU Lesser General Public License sites esd seocessus tue iawetendessenvetacdsaeceatesoecsae madeare 112 Appendix C Increasing memory for CytOScape cccececeeceneeceeeeceeeee ene eeeeseneesenseeeeseeeaenens 117 How to increase memory for Cytoscape icc cissesicctowut ncuaweieecannetieaseneahediautacsecssibachmsensaees 117 Changing memory allocations on Windows Mac and Linux machines 0ceeeeeeeees 118 Cytoscape 2 5 1 User Manual Cytoscape User Manual This document is licensed under the Creative Commons license 2006 Authors The Cytoscape Collaboration The Cytoscape project is an ongoing collaboration between Table 1 University of California at San Diego H Institute for Systems Biology E Memorial Sloan Kettering Cancer Center a Institut Pasteur g Agilent Technologies E University
38. E I E ET ee Geneieces 79 UE E E e I EE E EA E E AE EE EA E 80 Game T ee A T E 82 CSCIC E E E P V E O E E OT T O T O T E O T T 86 PGi NONO eaa E E E anne cenesanemnnccarscess 87 Pl uginsand the Plugin Manager ececirsreccisiendeee rror Eo EE ETE E EN EEEE ai 89 Toe Piae m AACE arser iarrar EREE TE E EOE 89 Get New T i A TE EAE ATE E N IAEE E T E E 89 Delet Existing PIUS INS serrera A E E EE i 90 Upate Sc FUSS corsier ie a Ese e ESEE 90 Download Plugins from a Custom S106 sciinen csodwascdensnnnegimevnsutasencneseedannedensnnreaadeneiuaxeanhedec 90 E EE E EE E A E SE E AOE A TEE 90 MNT a AMICI E E ET EE E S T A E E E ye 90 ASC T E EE E E E E A EE A A E A TAE AT E AN E E A 92 Rodine Dore esre on EE E E E 93 Whatis Level ot Detail LODI si scsccunsiicscwntscasnwstipacsouctstniwasiardeueedetaenwenrdsawntscersnmecscwets 93 PING EAL S a EE EAE A E E E O E O A EE is ecnatbare 94 Ontology and Annotation File Format ccccc cece eee ec eee ecee cess eens ee eeeeeeeeeeeeeeeeeeseeensenes 94 Node Name NT ayo cnanaeeeenacarconscamnssatenaneraneiae secscee x saaocantsadaganene capeansesanonanesase accutane 98 Import Ontology and Annotation icc cccovsssacseeadinsenceabadsewntons eres dbsancentacaesesatediaeelasarnsieedaes 100 Custom Annotation Files for Ontologies Other than GO for Advanced Users 0068 101 Ea En A E E cesta E E esa A E A A E E acess A E T 104 Adding or Removing Links as erescsrisrrsreriesrecrrierirrrrri inari sirke E
39. ND OR RE DISTRIBUTE THE LIBRARY AS PERMITTED ABOVE BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY GENERAL SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE LIBRARY INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POS SIBILITY OF SUCH DAMAGES END OF TERMS AND CONDITIONS Appendix C Increasing memory for Cytoscape How to increase memory for Cytoscape from Notes on memory consumption Cytoscape User Manual 117 Cytoscape User Manual For users interested in loading large networks the amount of memory needed by Cytoscape will increase Memory usage depends on both number of network objects nodes edges and the number of attributes Here are some rough suggestions for memory allocation Suggested Memory Size Without View Table 28 Number of Objects nodes edges Suggested Memory Size 0 70 000 512M default 70 000 150 000 800M Suggested Memory Size With View Table 29 Number of Objects nodes edges Suggested Memory Size 0 20 000 512M default 20 000 70 000 SOOM Changing memory allocations on Windows Mac and Linux machines There are a number of ways to change Cytoscape s memory allocation depending on your preferred method of opening the application All of t
40. Search terms are entered in the text box at the bottom For example to match any Node whose canonic alName starts with YDL you would select Node canonicalName and then type in YDL The is important as it matches any number of characters after YDL If you want to be more specific and only select nodes whose canonicalName starts with YDLOO followed by any other two characters you would type YDL00 The denotes any single character while the represents zero or more characters Full regular expression searching is supported although is not covered here Once the filter is defined it will be assigned a default descriptive name 84 Cytoscape User Manual Numerical Filter Use Filters Manage Filters Numeric Attribute Filter Create new Filter Remove selected Filter Available Filters Select All Filter Filter Name Node null 0 0 Node canonicalName YL Node canonicalName YC canonicalName a null 0 0 with a value For numeric attribute Select graph objects of type Node that is Apply selected Filter The Numerical Filter also allows you to filter nodes or edges and presents you with a list of available at tributes This filter matches all values in the network of your selecte
41. This only needs to be specified if Cytoscape can t find the web browser on your system Setting Default Properties It is possible to alter the default properties for Cytoscape Edit the properties via Edit Preferences Properties and check the Make Current Cytoscape Properties Default checkbox This will save the current properties to the cytoscape directory where they will then be applied to all of your Cytoscape sessions from that point on Otherwise Cytoscape will automatically save the properties used in a particular session inside its cys session file while the default properties will be applied at the beginning of subsequent sessions Managing Bookmarks Cytoscape contains a pre defined list of bookmarks which point to sample network files located on the Cytoscape web server Users may add modify and delete bookmarks through the Bookmark manager accessed by going to Edit Preferences gt Bookmarks amp Bookmark manager network yt Yeast Protein Protein Ideker T et al galFiltered Human Protein Protein HPRD Literature Curated In Human Protein Protein Rual et al Toward a proteo Human Protein Protein Rual et al Subnetwork For Human Protein Protein Stelzl et al A human proteir Yeast Protein Protein Ptacek et al Global analysis is FA There are currently two types of bookmarks network and annotation Network bookmarks are URLs pointing to network files available on the Internet
42. Type as Default Interaction will result in all interactions being given the value pp this value can be modified in Advanced Options below 4 Optional Define edge attribute columns if applicable Network table files can have edge attribute columns in addition to network data e Enable Disable Attribute Column By eft clicking on a column header in the preview table you can enable disable edge attributes If the header is checked and entries are blue the column will be im ported as an edge attribute For example the table below shows that columns 1 through 3 will be used as network data column 4 will not be imported and columns 5 and 6 will be imported as edge attributes galFilttered csy Column 1 amp Column 2 amp Column 3 x n4 attri attr 2 YER026C YGL122C pp FALSE abcd12345 1 2344543 YGR218W YGLOS7W pp TRUE abcd12346 1 2344543 YGLOD W YORZ04W pp TRUE abed12347 1 2344543 YLR2 49W YPROBOW pp TRUE abcd 12348 1 2344543 YLR249W YER118W pp TRUE abcd12349 1 2344543 YLR293C YGLOS W pp TRUE abed12350 1 2344543 YMR 146C YDR429C pp TRUE abcd12351 1 2344543 YDR429C YFLOI7C pp TRUE abcd 12352 12344543 YPROSBOW YAI 003W nn TRUE abrd17353 1 7344543 e Change Attribute Name and Data Types If you right click on a column header in the preview table you can modify the attribute name and data type For more detail see Modify Attribute Name Type below 5 Click the Import button 21 Cytoscape User Manual Advanced Opti
43. a delimiter between adjacent fields Every line of text is either the header line or contains all the measurements for a particular gene No name conversion is applied to expression data files The names given in the first column of the expression data file should match exactly the names used else where i e in SIF or GML files The first line is a header line with one of the following three header formats lt text gt lt text gt condl cond2 condl cond2 NumSigConds lt text gt lt text gt condl cond2 lt tab gt lt tab gt RATIOS lt tab gt lt tab gt LAMBDAS The first format specifies that both expression ratios and significance values are included in the file The first two text tokens in angled brackets contain names for each gene such as the formal and common gene names The condXx token set specifies the names of the experimental conditions these columns will contain ratio values This list of condition names must then be duplicated exactly each spelled the same way and in the same order Optionally a final column with the title NumSigConds may be present If present this column will contain integer values indicating the number of conditions in which each gene had a statistically significant change according to some threshold The second format is similar to the first except that the duplicate column names are omitted and there is no NumSigConds field This format specifies data with ratios but no significance v
44. a pupn ihat qaeri the cPach database ior ppecilied Anoma iiiara 1 0 LETH bd Pe BETE sian E canadai Released By Tip imga 03 F 0 1 ana Miui liyii 1 0 Crier pidik 2 0 Led Fata 2 0 Cr kpniker Lo Change hranlosd Site Deel ete Close The Currently Installed folder contains a number of default plugins that are fully integrated in every copy of Cytoscape as well as any additional installed plugins In contrast the Available for Install folder displays plugins that may be installed To install and use these plugins click on the file name and then click on the Install button at the bottom of the window A license agreement may appear in which case you must accept it in order to download the plugin You will then see a progress bar as the plugin is automatically downloaded and installed into your current version of Cytoscape The progress bar will disappear when the download is complete Other plugins can then be downloaded or the manager can be closed by clicking the Close button Once a new plugin is added it can immediately be used Closing and restarting Cytoscape is not required For example installing the MCODE plugin will automatically result in new menu options such as Plugins MCODE gt Start MCODE Troubleshooting 89 Cytoscape User Manual e If an installation error appears automatic installation of the plugin may not be supported To manually install the plugin go to the Cytoscape plugins page http cytosc
45. able 18 Edge Source and Target Arrow Color Table 19 Global Visual Properties Background Color Selected Node Color Selected Edge Color For each visual attribute you can specify a default value or define a dynamic visual mapping Cytoscape currently supports three different types of visual mappers 57 Cytoscape User Manual 1 Passthrough Mapper e The values of network attributes are passed directly through to visual attributes A passthrough mapper is only used to specify node edge labels For example a passthrough mapper can label all nodes with their common gene names 2 Discrete Mapper e Discrete network attributes are mapped to discrete visual attributes For example a discrete mapper can map all protein protein interactions to the color blue 3 Continuous Mapper e Continuous graph attributes are mapped to visual attributes Depending on the visual attribute there are three kinds of continuous mappers i Continuous to Continuous Mapper for example you can map a continuous numerical value to a node size ii Color Gradient Mapper This is a special case of continuous to continuous mapping Continuous numerical values are mapped to a color gradient iii Continuous to Discrete Mapper for example all values below 0 are mapped to square nodes and all values above 0 are mapped to circular nodes e However note that there is no way to smoothly morph between circular nodes and square nodes The t
46. able below shows visual mapper support for each visual property Legend Table 20 Symbol Mapping is not supported for the specified visual property X Mapping is fully supported for the specified visual property Mapping is partially supported for the specified visual property Support for continuous to continuous mapping is not supported Node Visual Mappings 58 Cytoscape User Manual Table 21 Node Visual Properties Pasthrough Mapper Discrete Mapper Continous Mapper ow peoo o o Perec RRS Perco ooo o o Permon RRS Smee ese Oi Perwse F ko ppo Perewa i or pesee Fi Pes F kooo pooo o Per ooo o p Peron k oo ooo pooo Node FontFanly ooo o o Edge Visual Mappings c gt lt gt lt lt gt lt lt gt lt X lt X lt XS Table 22 age Properties Pasthrough Mapper Discrete Mapper Continuous Mapper Color Be eo ooo o e Peman E o e Pesonn Rd A RRS e FRR agetabelGolr RRS Petwo Rid Rumec Benewah Perms ooo p e ine Bee Bielabel RRS Eeto i fdgeFonFanily SRS OX OX S S S OM OX OX m gt lt l m gt lt 59 Cytoscape User Manual Visual Styles Tutorials The following tutorials demonstrate some of the basic VizMapper features Each tutorial is independent of the others Tutorial 1 Create a Basic Visual Style and Set Default Values The goal of this tutorial is to learn how to create a new Visual Style and set
47. al Plugins and the Plugin Manager The Plugin Manager The Plugin Manager first introduced in Cytoscape 2 5 allows users to quickly and conveniently add extra features to Cytoscape directly from within Cytoscape eliminating the need for manual searches through different webpages to install and update plugins For plugin developer to enable automatic download of your plugin to Cytoscape users your plugin should be in compliance with Cytoscape 2 5 and the plugin jar zip files should be uploaded to the Cytoscape plugin web site at http cytoscape org plugins25 index php Note If you do not have Internet access enabled you will not see the list of available plugins or be able to automatically update existing ones however you will still be able to view and delete previously installed plugins Get New Plugins To install new features go to the Plugin Manager at Plugins gt Manage Plugins On the left side of the window that pops up you will see plugin folders labeled Currently Installed and Available for Install Double clicking on these will show sub folders and then the plugins themselves To find out more about a specific plugin click on its name to display some basic information on the right hand side of the window e are kanaga Piagine Plugins wwadlable for doweload from Cyioscace J Cumin inated 14 cPaih T o Core 14 Filet Laos 1 1 QukkFind 0 4 Yordan 5 SEM Menier 0 5 ePath 1 0 Caine Lieu 20 Dreigt P A D I
48. alues The third format specifies an MTX header which is a commonly used format Two tab characters precede the RATIOS token This token is followed by a number of tabs equal to the number of conditions followed by the LAMBDAS token This format specifies both ratios and significance values Each line after the first is a data line with the following format FormalGeneName CommonGeneName ratiol ratio2 lambdal lambda2 numSigConds The first two tokens are gene names The names in the first column are the keys used for node name lookup these names should be the same as the names used elsewhere in Cytoscape i e in the SIF GML or XGMML files Traditionally in the gene expression microarray community who defined these file formats the first token is expected to be the formal name of the gene in systems where there is a formal naming scheme for genes while the second is expected to be a synonym for the gene commonly used by biologists although Cytoscape does not make use of the common name column The next columns contain floating point values for the ratios followed by columns with the significance values if specified by the header line The final column if specified by the header line should contain an integer giving the number of significant conditions for that gene Missing values are not allowed and will confuse the parser For example using two consecutive tabs to indicate a missing value will not work the parser will regar
49. ame goID Appendix B GNU Lesser General Public License GNU LESSER GENERAL PUBLIC LICENSE e Version 2 1 February 1999 Copyright C 1991 1999 Free Software Foundation Inc 59 Temple Place Suite 330 Boston MA 02111 1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed This is the first released version of the Lesser GPL It also counts as the successor of the GNU Library Public License version 2 hence the version number 2 1 Preamble The licenses for most software are designed to take away your freedom to share and change it By contrast the GNU General Public Licenses are intended to guarantee your freedom to share and change free software to make sure the software is free for all its users This license the Lesser General Public License applies to some specially designated software packages typically libraries of the Free Software Foundation and other authors who decide to use it You can use it too but we suggest you first think carefully about whether this license or the ordinary General Public License is the better strategy to use in any particular case based on the explanations below When we speak of free software we are referring to freedom of use not price Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software and charge for this service if you wish that you receive source c
50. and Node Height mappings are ignored and Node Size overrides them If you want to use Fit node size to label function you need to unlock this Working with Continuous Mapping Editors There are three kinds of Continuous Mapping Editors Each of them are associated with a specific visual attributes Table 23 Editor Type Supported Data Type Visual Attributes Color Gradient Editor node edge border label colors Continuous Continuous Editor size width opacity Continuous Discrete Editor All others font shape text Range Setting Panel Range Setting 0 d Add Delete 7 2 3 Each editor has a common section named Range Setting 72 Cytoscape User Manual 1 Handle Value Box This box displays current value for selected slider handle Also you can directly type value in this box to move the slider to exact location 2 Add Handle Button Add a new handle to the editor 3 Delete Handle Button Delete selected handle from the slider widget Gradient Editor F a Gradient Editor for Node Color Continuous Mapping for Node Color q y V y gt 2 5000 10 0000 17 0000 Min 1 0 Degree Max 18 0 Range Setting 7s Add Delete Gradient Editor is a editor to create continuous mapping for colors To change the color of each region just double click the handles small triangles on the top Color gradient will be created only when editor has two or more handles see the example below Table 24 1 Sl
51. and moving the mouse You can also pan the image by holding down the left mouse button over the blue box in the Network Overview panel in the lower left hand of the Cytoscape desktop Other Mouse Behaviors Select Click the left mouse button on a node or edge to select that object You can hold down the Shift key to select more than one node edge or you can hold down the left mouse button and drag the mouse to select groups of nodes edges 36 Cytoscape User Manual Context Click the right mouse button on a node edge to launch a context sensitive menu with additional information about the node edge Automatic Layout Algorithms The Layout menu has an array of features for organizing the network visually according to one of several algorithms aligning and rotating groups of nodes and adjusting the size of the network Most of these features are available from plugins that are packaged with Cytoscape 2 3 and above Some of the layout algorithms provided are Cytoscape Spring Embedded Layout The spring embedded layout is based on a force directed paradigm Network nodes are treated like physical objects that repel each other such as electrons The connections between nodes are treated like metal springs attached to the pair of nodes These springs repel or attract their end points according to a force function The layout algorithm sets the positions of the nodes in a way that minimizes the sum of forces in the network This al
52. anguage GML or gml format e XGMML extensible graph markup and modelling language e SBML e BioPAX e PSI MI Level 1 and 2 5 e Delimited text e Excel Workbook xls The SIF format specifies nodes and interactions only while other formats store additional information about network layout and allow network data exchange with a variety of other network programs and data sources Typically SIF files are used to import interactions when building a network for the first time since they are easy to create in a text editor or spreadsheet Once the interactions have been loaded and network layout has been performed the network may be saved to GML or XGMML format for interaction with other systems All file types listed except Excel are text files and you can edit and view them in a regular text editor 23 Cytoscape User Manual SIF Format The simple interaction format is convenient for building a graph from a list of interactions It also makes it easy to combine different interaction sets into a larger network or add new interactions to an existing data set The main disadvantage is that this format does not include any layout information forcing Cyto scape to re compute a new layout of the network each time it is loaded Lines in the SIF file specify a source node a relationship type or edge type and one or more target nodes nodeA lt relationship type gt nodeB nodeC lt relationship type gt nodeA nodeD lt relationshi
53. annot contain an equals sign and no guarantees are made concerning leading or trailing whitespace Object names must be the Node ID or Edge ID as seen in the left most column of the attribute browser if the attribute is to map to anything These names must be reproduced exactly including case or they will not match Edge names are all of the form sourceName edgeType targetName Specifically that is 28 Cytoscape User Manual Table 10 sourceName space openParen edgeType closeParen space targetName Note that tabs are not allowed in edge names Tabs can be used to separate the edge name from the delimiter but not within the edge name itself Also note that this format is different from the specification of interactions in the SIF file format To be explicit a SIF entry for the previous interaction would look like won sourceName edgeType targetName Or Table 11 sourceName whiteSpace edgeType whiteSpace targetName To specify lists of values use the following syntax listAttributeName class java lang String firstObjectName firstValue secondValue thirdValue secondObjectName onlyOneValue This example shows an attribute whose value is defined as a list of text strings The first object has three strings and thus three elements in its list while the second object has a list with only one element In the case of a list every attribute value uses list syntax i e parentheses and each element is of the same
54. ape org plugins25 index php scroll down to find the plugin click on the appropriate link to download the file and then save it in the Cyto scape plugins folder on your hard drive e If the new plugin does not automatically work you may need to restart Cytoscape e If the plugin does not appear in the Currently Installed folder of the Plugin Manager then Cytoscape was unable to load the plugin Your command line will display the error message generated Delete Existing Plugins To delete an existing plugin go to the Plugin Manager at Plugins gt Manage Plugins click on the appro priate plugin once to select it and then click the Delete button at the bottom of the manager It is best to avoid deleting core plugins as this may cause Cytoscape or other plugins to malfunction A plugin will be completely deleted after you have restarted Cytoscape Update Existing Plugins Going to Plugins gt Update Plugins will result in Cytoscape automatically accessing the Internet to look for updated versions of the plugins you have installed If newer versions are available Cytoscape will then display the available updates in the Plugin Manager otherwise it will inform you that there are no updatable plugins When multiple updates are detected you will have the option to download some or all of the updates Some updates may require re accepting the license before the download will begin All updates require Cytoscape to be restarted in order
55. ape session files so changes to general properties will be saved as part of the current session but will only carry over to subsequent sessions if they are set as defaults or exported using the File Export function Cytoscape properties are configurable via Add Modify and Delete operations 4 cCytoscape Preferences Editor Properties Property Name bioDataserver Pleasespecity canonicalizeNames true cytoscape version num 2 5 defaultSpeciesName Saccharomyces cerevisiae defaultVisuastye default expormtTextAsshape true maximizeVviewOnCreate false MOTE Changes to these properties are used in the current session ONLY unless otherwise specified below Default Visual Styles Only check this option if you want the current Wisual styles to be defaults in ALL future cytoscape sessions Your current visual styles are automatically Saved in your Cytoscape session file and won t be lost Make Current Visual Styles Default Default Cytoscape Properties Only check this option if you want the current Cytoscape properties to be defaults in ALL future cytoscape sessions Your current Cytoscape properties are automatically saved in your Cytoscape session file and won t be lost Make Current Cytoscape Properties Default 16 Cytoscape User Manual Some common properties are described below Table 9 Property name Default value Valid values defaultWebBrowser A path to the web browser on your system
56. ation Annotations in Cytoscape are stored as a set of ontologies e g the Gene Ontology or GO An ontology consists of a set of controlled vocabulary terms that annotate the objects For example using the Gene Ontology the Saccharomyces Cerevisiae CDCS55 gene has a biological process described as protein bio synthesis to which GO has assigned the number 6412 a GO ID GO 8150 biological_process GO 7582 physiological processes GO 8152 metabolism GO 44238 primary metabolism GO 19538 protein metabolism GO 6412 protein biosynthesis Graphical View of GO Term 6412 protein biosynthesis solocicat process a process i metabolism primary metabolism biosynthesis ie a A protein metabolism Fa ipi k F h Y i protein blosynthesis Cytoscape can use this ontology DAG Directed Acyclic Graph to annotate objects in networks The On tology Server originally called BioDataServer is a Cytoscape feature which allows you to load navigate and assign annotation terms to nodes and edges in a network Cytoscape 2 4 now has an enhanced GUI for loading ontology and associated annotation enabling you to load both local and remote files Ontology and Annotation File Format The standard file formats used in Cytoscape Ontology Server are OBO and Gene Association The GO website details these file formats e Ontologies and Definitions http www geneontology org GO downloads shtml ont e Current Annotations
57. bute floating point attribute YJRO22W YNRO53C pp TRUE abed12371 1 2344543 YER116C YDLO13W pp TRUE abed12372 1 2344543 YNL307C YALO38W pp FALSE abcd12373 1 2344543 YNL216W YCRO12W pd TRUE abed12374 1 2344543 YNL216W YGR254W pd TRUE abed12375 1 2344543 The network table files should contain at least two columns source nodes and target nodes The interaction type is optional in this format Therefore a minimal network table looks like the following YJR022W YNRO53C YER116C YDLO13W NL307C YALO38W NL216W YCRO12W NL216W YGR254W KK K One row in a network table file represents an edge and its edge attributes This means that a network file is considered a combination of network data and edge attributes A table may contain columns that aren t meant to be edge attributes In this case you can choose not to import those columns by clicking on the column header in the preview window This function is useful when importing a data table like the following Unique ID A Unigue ID B Alternative ID A Alternative ID B Aliases A Aliases B Interaction detection methods First author surnames Pubmed IDs species A 7205 5747 TRIP6 PTK2 015654 005397 1 vv HPRD Currently not available 14688263 15892868 Marcotte Mammalia Homo sapiens protein protein HPRD Marcotte 0 Thyro 20 Cytoscape User Manual 4174 7311 MCM5 UBA52 P33992 P62987 neighbouring_reaction Currently not available 15608231 Reactome Homo sapiens Homo sapiens protein protein Reactome 1
58. butes loaded onto Cytoscape networks to properties you specify For example you can select all the nodes whose 79 Cytoscape User Manual name contains a specific pattern or whose numeric attribute value falls within a certain range Cytoscape provides filters as a core plugin Users can perform complex selection by defining basic filters selection based on a single attribute and compound or Boolean filters combining basic filters for selection based on multiple attributes Based on feedback from Cytoscape users the Cytoscape team has determined that it is necessary to redesign the user interfaces for the filters The newly designed filters will preserve all the functionality of the old filters while introducing more user friendly interfaces As this process is not yet complete Cytoscape 2 5 contains both the old filters and a preliminary version of the new filter interfaces Eventually the old filters will be replaced by the new filters Using New Filters By default you should see a filter icon on the toolbar SA If you click on it the filters tab on the Control Panel at the left of the screen will be selected You can also access the filters by clicking directly on the tab or by using the Select Use Filters menu option The filters tab initially looks like this 1 Create a filter To create a filter click the option button and select Create new filter from the list provided Enter a name
59. by the midpoint between the top and bottom most nodes Vertical Align Bottom The bottoms of the selected nodes are aligned with the bottom most node Horizontal Align Center The centers of the selected nodes are aligned along a line defined by the midpoint between the left and right most nodes Horizontal Align Left The left hand sides of the selected nodes are aligned with the left most node Horizontal Align Right The right hand sides of the selected nodes are aligned with the right most node 42 Cytoscape User Manual Table 14 Description of Distribute Options fore Vertical Distribute Top The tops of the selected nodes are distributed evenly between the top most and bottom most nodes which should stay stationary Vertical Distribute Center The centers of the selected nodes are distributed evenly between the top most and bottom most nodes which should stay stationary Vertical Distribute Bottom The bottoms of the selected nodes are distributed evenly between the top most and bottom most nodes which should stay stationary Horizontal Distribute Left The left hand sides of the selected nodes are distributed evenly between the left most and right most nodes which should stay stationary Horizontal Distribute Center The centers of the selected nodes are distributed evenly between the left most and right most nodes which should stay stationary Horizontal Distribute Right The right hand sides of the s
60. ch as Delete Selected Node Edges Copy To New Network and Invert Selection The Select Menu The Select Nodes and Select Edges menus provide several mechanisms for selecting nodes and edges Most options are fairly straightforward however some need extra explanation Select Nodes gt By Name selects nodes by the node identifier ID This is the value seen in the leftmost column of the attribute browser This does not change even if the displayed node label changes Select Nodes From File selects nodes based on node identifiers found in a specified file The file format is simply one node id per line Nodel Node2 Node3 86 Cytoscape User Manual Editing Networks Using Cytoscape s Editor you can build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window The palette contains a set of shapes for nodes and arrows for edges The shapes on the palette are defined by the current Visual Style with Node Shape and Node Color mapping into the shape and color of a node and Edge Target Arrow mapping into the target arrow of an edge An example of an editor with the palette contained in CytoPanel 1 is shown below a Cytoscape Version 2 5 File Edit View Select Layout Plugins Help i aoe Cytoscape Desktop New Session 2GQQnagaks Control Panel da ee Network 0 t Network VizMapper Editor Filters Directed Edge F Add a N
61. ch box empty and click on the down arrow directly next to the search box Cytoscape will provide you with an initial list of matches In the case below we will get a list of all distinct cellular locations in the network extracellular region mitochondrial intermembrane s 1 hit mitochondrial outer membrane 29 hits 15 hits Dynamic Filtering via Quick Find If you choose to index on a numerical attribute the Quick Find search box changes to a dynamic slider for quick filtering For example 1 Import a network such as sampleData galFiltered sif using File gt Import Network multiple file types 78 Cytoscape User Manual 2 Import an expression data file such as sampleData galExpData pvals using File Import gt Attribute Ex pression Matrix 3 Configure Quick Find to index the network using the gall RGExp attribute AOO Configure Search Options for galFiltered sif Select Index Type Index Nodes Index Edges Select Attribute Search on Attribute gallRGexp Attribute Description No description available Sample Attribute Values 0 045 0 963 0 101 0 551 0 165 Me 4 Use the slider widget to automatically filter the entire network default KH Select EED LEEN EE 1 102 035 w Se gc Sion ae vik he yy t gt og gk Filters Filters allow you to quickly select multiple nodes or edges of interest by comparing node and edge attri
62. d attribute that are greater than less than or equal to a number you type in the search box Node Topology Filter Use Filters Manage Filters Node Topology Filter Create new Filter Remove selected Filter Available Filters Filter Name NodeTopology Select All Filter Node canonicalName YL eE Ai eee Node canonicalName YOY i Node canonicalName Node null o 0 within distance NodeTopology that pass the Filter Select All Filter x Apply selected filter The node topology filter allows you to select all nodes selected by a preexisting filter and having n neigh bours found at a distance of m or fewer edges away For instance to select all the nodes adjacent to a node with the canonical name matching YD you would select nodes with 1 neighbors within distance 1 that pass the filter Node canonicalName YD The node topology filter depends on the existence of other filters By default No Filter is selected it doesn t filter out anything but rather selects all nodes 85 Cytoscape User Manual Boolean Filter Use Filters Manage Filters Boolean Meta Filter Create new Filter Remove selected Filter _ Filter Name BooleanMeta Available Filters Select objects that pass ALL i of the
63. d both tabs as a single delimiter and be unable to parse the line correctly Optionally the last line of the file may be a special footer line with the following format NumSigGenes intl int2 35 Cytoscape User Manual This line specified the number of genes that were significantly differentially expressed in each condition The first text token must be spelled exactly as shown the rest of the line should contain one integer value for each experimental condition Navigation and Layout Basic Network Navigation Zoom Pan Cytoscape uses a Zoomable User Interface for navigating and viewing networks ZUIs use two mechanisms for navigation zooming and panning Zooming increases or decreases the magnification of a view based on how much or how little a user wants to see Panning allows users to move the focus of a screen to dif ferent parts of a view Cytoscape provides two mechanisms for zooming either using mouse gestures or buttons on the toolbar Use the zooming buttons located on the toolbar to zoom in and out of the interaction network shown in the current network display Zoom icons are detailed below QQQa From Left to Right e Zoom Out e Zoom In e Zoom Selected Region e Zoom Out to Display all of Current Network You can also zoom in out by holding down the right mouse button and moving the mouse to the right zoom in or left zoom out You can pan the network image by holding down the middle mouse button
64. de spaces in your property simply enclose the name and value in quotation marks cytoscape sh P defaultSpeciesName Homo Sapiens The property option subsumes previous options noCanonicalization species and bioDataServer Now it would look like cytoscape sh P defaultSpeciesName Human P noCanonicalization true P bioDataServer myServer V vizmap lt file gt This option specifies a visual properties file All options described above including plugins can be loaded from the GUI once Cytoscape is running 15 Cytoscape User Manual Cytoscape Preferences Managing Properties Table 8 Important If you have used previous versions of Cytoscape you will notice that handling of properties has changed The most important change is that properties are no longer saved by default to the current directory or to your home cytoscape directory Properties are stored by default in Cytoscape session files cys extension The cytoscape props file still exists in the cytoscape directory but is only written to when the user explicitly requests that the current settings be made the defaults for all future sessions of Cytoscape Unless you have something important in your cytoscape cytoscape props file your best bet will be to delete the file and use the defaults The Cytoscape Properties editor accessed via Edit Preferences Properties is used to specify general and default properties Properties are now stored in Cytosc
65. de width and height When node size is unlocked AND Node Width Height discrete mappings are available you can fit the size of each node to label automatically by selecting this function See the example below 71 Cytoscape User Manual i Ha 25 Cre OLE why r f x d ii ii aa aaa Pienmis SAO O A Y areia LIGE LA iroh Ain maaa a at fi F rr pasma green LILA OLA YLES i nN component WUE A Fan 4 aA 7 peoieenal protean 245 a N f transcription factor fo ribosomal protein 24 4 mm ay e PU pr F rs an hatidinal dekydrogenase F lamin irensonpibon buiw i aoe Bho elo phanita kio protein f Bi _ i T F E E r ant i k i eee aces p meuvaie decarbomplase ie rescpomal protein Lie iret BB a 9 i l u e F ee ae pe r j p i ai a Po i a hoppy poyin LISA BPA p UDP glucose 4 e5 enerase i i K B TT T ra eee ibceomal protein 174 mp3 LA i ris ii Tarai pe ea Peer F T TT B i pi fi e Modify Discrete Values Currently this is only for colors You can change overall brightness for discrete color mappings Edit Selected Values at Once You can set multiple values at once First you need to select rows you want to change values then select Edit selected values at once A dialog pops up and you can enter the new value for the selected rows Lock Node Width Height If this menu item is checked Node Width
66. dification are not covered by this License they are outside its scope The act of running a program using the Library is not restricted and output from such a program is covered only if its contents constitute a work based on the Library independent of the use of the Library in a tool for writing it Whether that is true depends on what the Library does and what the program that uses the Library does 1 You may copy and distribute verbatim copies of the Library s complete source code as you receive it in any medium provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty keep intact all the notices that refer to this License and to the absence of any warranty and distribute a copy of this License along with the Library You may charge a fee for the physical act of transferring a copy and you may at your option offer warranty protection in exchange for a fee 113 Cytoscape User Manual 2 You may modify your copy or copies of the Library or any portion of it thus forming a work based on the Library and copy and distribute such modifications or work under the terms of Section 1 above provided that you also meet all of these conditions a The modified work must itself be a software library b You must cause the files modified to carry prominent notices stating that you changed the files and the date of any change c You must cause the whole of the work to be
67. e rge k m l pale dees ee bie ar ey wus eer rae ILE epg prea me ese epee ee l pram n e Visualize gene expression data along a color gradient 49 Cytoscape User Manual e Control edge transparency opacity using edge weights 50 Cytoscape User Manual 51 Cytoscape User Manual The VizMapper can be accessed by going to View Open VizMapper or by clicking on the VizMapper 1 O n BS Also starting in Cytoscape 2 5 direct access to the VizMapper is provided via a tab on the Control Panel at the left hand side of the screen formerly known as CytoPanel 1 Introduction to the VizMapper User Interface As of Cytoscape 2 5 the VizMapper has undergone a complete interface redesign There are three types of components in the new VizMapper 1 Main Panel e a a Fy FS FY Control Panel Network VizMapper Editor Filters Current Visual Style Sample3 Defaults Visual Mapping Browser DIAMOND PARALLELOGRAM Node Tooltip canonicalName Node Color gal4RGexp Mapping Type Continuous Mapping Graphical View F Edge Visual Mapping Edge Color interaction Mapping Type Discrete Mapping pd pp e This panel allows you to create delete view switch between different visual styles using the Current Visual Style options The Visual Mapping Browser at the bottom displays the mapping details for a given visual style and is used to edit these details as well
68. e window is similar to that of the Import Network from Table window 1 Select File Import Attribute from Table text MS Excel 30 Cytoscape User Manual 2 Select one of the attribute types from the Attributes radio buttons Cytoscape can import node edge and network attributes 3 Select a data file To load a local file click on the Select File button and choose a data file This can be either a text or Excel xls file To load a remote file type the source URL directly into the text box To show a preview of the remote file click the Reload button on the Show Text File Import Options panel 4 Optional If the table is not properly delimited in the preview panel change the delimiter in the Text File Import Options panel The default delimiter is the tab This step is not necessary for Excel Work books 5 By default the first column is designated as the primary key Change the key column if necessary Annotation File to Attribute Mapping Key Column in Annotation File Primary Key dh GENE w 6 Click the Import button Advanced Options Mapping Key Attributes to the primary key Aliases Formerly Cytoscape only supported mapping between node edge IDs and the primary keys in attribute files With the introduction of Cytoscape 2 4 this limitation has been removed and now both IDs and at tributes with primitive data types string boolean floating point and integer can be selected as the Key Attr
69. e combined with the library in order to run GNU LESSER GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING DISTRI BUTION AND MODIFICATION 0 This License Agreement applies to any software library or other program which contains a notice placed by the copyright holder or other authorized party saying it may be distributed under the terms of this Lesser General Public License also called this License Each licensee is addressed as you A library means a collection of software functions and or data prepared so as to be conveniently linked with applic ation programs which use some of those functions and data to form executables The Library below refers to any such software library or work which has been distributed under these terms A work based on the Library means either the Library or any derivative work under copyright law that is to say a work containing the Library or a portion of it either verbatim or with modifications and or translated straightfor wardly into another language Hereinafter translation is included without limitation in the term modific ation Source code for a work means the preferred form of the work for making modifications to it For a library complete source code means all the source code for all modules it contains plus any associated interface definition files plus the scripts used to control compilation and installation of the library Activ ities other than copying distribution and mo
70. e visualized in a user defined way by setting up a mapping from data attributes to visual attributes colors shapes and so on The section on visual styles discusses this in greater detail Cytoscape Attribute File Format Node and edge attribute files are simply formatted a node attribute file begins with the name of the attribute on the first line note that it cannot contain spaces Each following line contains the name of the node followed by an equals sign and the value of that attribute Numbers and text strings are the most common attribute types All values for a given attribute must have the same type For example FunctionalCategory YALO01C metabolism YARO02W apoptosis YBLO07C ribosome An edge attribute file has much the same structure except that the name of the edge is the source node name followed by the interaction type in parentheses followed by the target node name Directionality counts so switching the source and target will refer to a different or perhaps non existent edge The fol lowing is an example edge attributes file InteractionStrength YALOO1C pp YBRO43W 0 82 YMRO22W pd YDL112C 0 441 YDL112C pd YMRO22W 0 9013 Since Cytoscape treats edge attributes as directional the second and third edge attribute values refer to two different edges source and target are reversed though the nodes involved are the same Each attribute is stored in a separate file Node and edge attribute file
71. e_2 0A 0000441 node_3 0A 0000702 where OA_ represents an ontology term ID This example is a file with the minimum necessary number of columns however you can include additional columns that will appear as additional node attributes Some ontologies will be used to annotate edges or networks For example the Protein protein interaction ontology is a controlled set of terms for annotating interactions between proteins so ontology terms should be mapped onto edges see example below node_l pp node_2 MI 0445 node_3 pp node_l MI 0046 node_2 pp node_3 MI 0346 103 Cytoscape User Manual Import nrag Gata and Annatons Import Ontology and Annotation Anribites Hode a Edge Hehaork Annotation amp Local Annotation File edgeAssociation txt Ontology Protein protein interaction Advarard ShowMapping Options Show Text File import Options _ import everything vathout checking maiches Cene Association only Annotelion File to Agibude Wanping Key Cabumn i Annolation File Key Amibe for Network Aliag Column Attribute Mame Dare Type Primary Key lp Column 1 op w0 lwmn 1 diy String PFI Ontology dip String Annactation file te Onielagy Mapping Key Column in Annotation File Ontology Column 2 Protein protein interaction Preview Text File Left Click Enable Disable Column Right Click Edit Column Legend MES edged ssociation tet Ontology key
72. ea p l Lapeet J Miad Aric 5 us I ea Alpe ard Deviniteate YREOTSC Laipa Goeth Ae oe P LUI eg eatin SUA DSS Wah idence fue uae Le ee cee WPRO2SC Cyl Abate aed ats propin inane id raha te Cee ol PAAHDA n BL Ragin TPH oe pi Alga YOLGS1LW Dompig bre Maa nomics remir cur Frac Peden a Goes lz 5 m YLEADOW Puan bbc aber Aer KHA eesyer ESS erie acre a GMA ai a al a Te da WPLZOW CAMP Cepia pbn kira GE i Ros pegina Dga eardiation proteins OAM gapen peoiein kirp i Chseribute TMAJ GW Sober 17 ba ef TT aad SA comal jGl ippoig erie i ete cede A eel ne a ine TORSON Tabea of EH aad abeo ee a a A of a en a randy TPH ee reptile b ya Ty YRRL9S hott ig kDa of TD ond SAA comal HEL ipenc furnigrigton in meses cel gy A compe We CAD i Dee ee ee HA SATA bihag E a a oe ttt fee teen te Sari FLEIS2C wl iton owen ied mandate leering of 20 cece rAMA Genen om haai baon inmates fan as 4 a t E k O88SQQQQuQurrreeeeeeeeeeeeeyE EEeEeEEoEooooo deska ni Edge Annib Boere Mierer Aunribute Beatet Wicana bo Ceteicage 2 5 Aighe click drag to MOi bidit click dra bo FAH The user can then choose to resize hide or float CytoPanels For example in the screenshot below the user has chosen to float all panels and toolbar 91 Cytoscape User Manual Crip Venn ES Fie Dat ew fete ui Fapa Hg l F Ha Fo ey raach Gakk Certain peeing cyl a Pt ie weeds be a
73. ease data integration This ontology is used to annotate biological processes pathways and sub pathways in the INOH pathway data INOH is part of the BioPAX working group Protein protein interaction A structured controlled vocabulary for the annotation of experiments concerned with protein protein interactions Pathway Ontology The Pathway Ontology is a controlled vocabulary for pathways that provides standard terms for the annotation of gene products PATO PATO is an ontology of phenotypic qualities intended for use in a number of applications primarily phenotype annotation For more information please visit the PATO wiki http www bioontology org wiki in dex php PATO Main_Page Mouse pathology The Mouse Pathology Ontology MPATH is an ontology for mutant mouse pathology This is Version 1 Human disease This ontology is a comprehensive hierarchical controlled vocabulary for human disease representation For more information please visit the Disease Ontology website http diseaseontology sourceforge net Although Cytoscape can import all kinds of ontologies in OBO format annotation files are associated with specific ontologies Therefore you need to provide the correct ontology specific annotation file to annotate nodes edges networks in Cytoscape For example while you can annotate human network data using the GO Full ontology with human Gene Association files you cannot use a combination of the human Disease Ontolog
74. ee iF ri r Dii Ta LF pw o te CY oe fay Fe 3 a SHASENMaeak is oe Ft Me besgi Y i Fara HE Chet er Bei a D Epi Vaa ater le k a 4 F E i hiesa Bp rea i i 3 ee 1i ALi i i o E4 Aa 1 Corea a a E TA pip Hi m F gt 4 F 2 ET Te e i ih ar k ia gt a i f m i 7 Piisi Migh any bees k a b z F i a i H A 7 E T hodn Yean Heep m Fj i i PEI F nice DUN tro ode Cor TACO earn ou r EREA i 4 Mannng Tapa oro Happy E r het wi 57 at b a LATE y fe 3 f e f 4 hi l H Crap Yre L a E b ri Reed Face i EE n E OR te a F ete Fip BA ia A E E E E e i 5 a Pi Teper Irje Saree Wih Aj Jija iL ee DO Gane s r 4 al T T ii C a i Terg O se EE rT T Leelee nd gt Gud L ik H E ms a T Lege Pose deh tnlr Borde er a d E Ez i eae ae rors Se eg a J ee ee eT a ay a Fa AT pn TL ST Seth Pa er nit TETS Ab bP ae kiaiii ete MH GA ee LA piima tiaras Lay a kadi Lida TL ete Beep este that i Darter Toei of enor i HE LHET Wee Lea a a pce Mk PR eae m Pp ah a i krade Powe Fler TRohw A ieee reer Se ete a e Derkdetteer bi Bere ip ieee j Het mph bod jarhat pipir e P THIS ovens cf tae feet betes Sas DA ue Doba ea od da eget h A rice con broach Foe Tata Thi Ti ee ee eee ee ee et as pe Pate el AE els kadr Loder Cie YONE Ty et et me k CAA ma Taki Seve HAE L ie o THIG igir a al upi b iir A Saji s pf ees g ee e ri
75. elect from pull down menu Drag amp Drop URL from Web Browser Importing networks from URL addresses has an important caveat Because Cytoscape determines file type primarily not exclusively by file extension it can have trouble importing networks with URLs that don t end in a human readable file name If Cytoscape does not recognize a meaningful file name and extension in the URL it will attempt to guess the type of file based on MIME type If the MIME type is not recog nizable to any of our import handlers then the import will fail Another issue for network import is the presence of firewalls which can affect which files are accessible to a computer To work around this problem Cytoscape supports the use of proxy servers To configure the proxy server go to Edit Preferences Proxy Server This is further described in the Preferences chapter Import Free Format Table Files Introduced in version 2 4 Cytoscape now supports the import of networks from delimited text files and Excel workbooks using Edit Import Network from Table Text MS Excel An interactive GUI allows users to specify parsing options for specified files The screen provides a preview that shows how the file will be parsed given the current configuration As the configuration changes the preview updates automatically In addition to specifying how the file will be parsed the user must also choose the columns that represent the Source nodes the Target n
76. elected nodes are distrib uted evenly between the left most and right most nodes which should stay station Table 15 Description of Stack Options Vertical Stack Left Vertically stacked below top most node with the left hand sides of the selected nodes aligned Vertical Stack Center Vertically stacked below top most node with the centers of selected nodes aligned Vertical Stack Right Vertically stacked below top most node with the right hand sides of the selected nodes aligned Horizontal Stack Top Horizontally stacked to the right of the left most node with the tops of the selected nodes aligned Horizontal Stack Center Horizontally stacked to the right of the left most node with the centers of selected nodes aligned Horizontal Stack Bottom Horizontal Stack Center Horizontally stacked to the right of the left most node with the bottoms of the selected nodes aligned Edge Handles This is a little known feature If you select an edge and then Ctrl left click on the edge an edge handle will appear This handle can be used to change the shape of the line To remove a handle simply Ctrl left click on the handle again Table 16 Straight Edge Smooth Edge Two other options under Select Edges provide further control Smooth Selected Edges turns an edge consisting of line segments into a smoothed bezier curve and Straighten Selected Edges turns a curved edge back into line segments 43 Cytoscape Us
77. er Manual View RAEI Layout Plugins Help Mouse Drag Selects A Q Nodes Search ETE ver selection xi E Hide selection AH Select all nodes and edges ANA Show All XOH Deselect All Nodes and Edges tA Select all edges YA Use Filters F7 Deselect all edges XA Smooth selected edges Straighten selected edges Node Movement and Placement In addition to the ability to click on a node and drag it to a new position Cytoscape now has the ability to move nodes using the arrow keys on the keyboard By selecting one or more nodes using the mouse and clicking one of the arrow keys lt gt T J the selected nodes will move one pixel in the chosen direction If an arrow key is pressed while holding the Shift key down the selected nodes will 10 pixels in the chosen direction Mouse movement has also been enhanced If the Shift key is held down while dragging a node the node will only move horizontally vertically or along a 45 degree diagonal Visual Styles What is a Visual Style One of Cytoscape s strengths in network visualization is the ability to allow users to encode any attribute of their data name type degree weight expression data etc as a visual property such as color size transparency or font type A set of these encoded or mapped attributes is called a Visual Style and can be created or edited using the Cytoscape VizMapper With the VizMapper the visual appearance of your network is easily customized For
78. expression values one per experiment These can be either absolute expression values or fold change ratios Each experiment is identified by its experiment name given in the first line Optionally significance measures such as P values may be provided These values generated by many microarray data analysis packages indicate where the level of gene expression or the fold change appears to be greater than random chance If you are using significance measures then your expression file should contain them in a second set of columns after the expression values The column names for the expression significance measures need to match those of the expression values exactly 33 Cytoscape User Manual For example here is an excerpt from the file galExpData pvals in the Cytoscape sampleData directory GENE COMMON gallRG gal4RG gal80R gallRG gal4RG gal80R YHROSIW COX6 0 034 0 111 0 304 3 75720e 01 1 56240e 02 7 91340e 06 YHR124W NDT80 0 090 0 007 0 348 2 71460e 01 9 64330e 01 3 44760e 01 YKL181W PRS1 0 167 0 233 0 112 6 27120e 03 7 89400e 04 1 44060e 01 YGRO72W UPF3 0 245 0 471 0 787 4 10450e 04 7 51780e 04 1 37130e 05 This indicates that there is data for three experiments gall RG gal4RG and gal80R These names appear two times in the header line the first time gives the expression values and the second gives the significance measures For instance the second line tells us that in Experiment gall RG the gene YHRO51W has an expression
79. ferent file format than normal attributes however the resulting attributes are not treated differently by Cytoscape Gene expression data like attribute data can be loaded at any time but are generally only relevant once a network has been loaded Data File Format Gene expression ratios or values are specified over one or more experiments using a text file Ratios result from a comparison of two expression measurements experiment vs control Some expression platforms such as Affymetrix directly measure expression values without a comparison The file consists of a header and a number of space or tab delimited fields one line per gene with the following format Identifier CommonName valuel value2 valueN pvall pval2 pvalN Brackets indicate fields that are optional The first field identifies which Cytoscape node the data refers to In the simplest case this is the gene name exactly as it appears on the network generated by Cytoscape case sensitive Alternatively this can be some node attribute that identifies the node uniquely such as a probeset identifier for commercial microar rays The next field is an optional common name It is not used by Cytoscape and is provided strictly for the user s convenience With this common name field the input format is the same as for commonly used ex pression data anaysis packages such as SAM http www stat stanford edu tibs SAM The next set of columns represent
80. for the update to be fully installed After clicking the Update All or Update Selected buttons a progress bar will appear showing the status of the download it will disappear once the update is complete and the Plugin Manager can then be closed by clicking the Close button Note The Update All button will update all listed plugins to the newest available version If you prefer a different version select the name and click Update Selected Download Plugins from a Custom Site The Plugin Manager automatically connects to the Cytoscape website and the sites of registered Cytoscape plugins to check for and download any available plugins and updates To change this setting open the Plugin Manager by going to Plugins gt Manage Plugins and click the Change Download Site button You will be asked to choose a site from a preset list of bookmarks Select one and click Ok Alternatively click the Add Site button to open the Bookmark Manager and modify the list of bookmarks In the Bookmark Manager choose the plugins category from the dropdown list and then add edit delete URLs using the appropriate buttons on the right hand side of the window After the correct site is selected set it as the download site by clicking OK The Plugin Manager will refresh using that site Note Custom download sites added from the Plugin Manager will not be saved when you exit Cytoscape CytoPanels What are CytoPanels CytoPanels are floatable dockable panels desig
81. ftware distribution system which is implemented by public license practices Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system it is up to the author donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice 116 Cytoscape User Manual This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License 12 If the distribution and or use of the Library is restricted in certain countries either by patents or by copyrighted interfaces the original copyright holder who places the Library under this License may add an explicit geographical distribution limitation excluding those countries so that distribution 1s permitted only in or among countries not thus excluded In such case this License incorporates the limitation as if written in the body of this License 13 The Free Software Foundation may publish revised and or new versions of the Lesser General Public License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns Each version is given a distinguishing version number If the Library specifies a version number of this License which applies to it and any later version you have the option of following the terms and conditio
82. g the new formats OBO Gene Association described in the previous section since they are easier to download directly from the Gene Ontology project and use directly Currently users have no access to an import interface for this old format Building your own annotation files The annotation server requires that the gene annotations and associated ontology of controlled vocabulary terms follow a simple format This simple format was chosen because it 1s efficient to parse and easy to use The flat file formats are explained below The Ontology Format By example the Gene Ontology GO curator G0 type all 0003673 Gene_Ontology 106 Cytoscape User Manual 03674 molecular_function partof 0003673 08435 anticoagulant isa 0003674 16172 antifreeze isa 0003674 16173 ice nucleation inhibitor isa 0016172 16209 antioxidant isa 0003674 45174 glutathione dehydrogenase ascorbate isa 0009491 0015038 0016209 0016672 04362 glutathione reductase NADPH isa 0015038 0015933 0016209 0016654 17019 myosin phosphatase catalyst partof 0017018 gt gt m E ee E oe SD O OO OOO SO OD A second example KEGG pathway ontology curator KEGG type Metabolic Pathways 90001 Metabolism 800 Carbohydrate Metabolism isa 90001 800 Lipid Metabolism isa 90001 800 Energy Metabolism isa 90001 800 ucleotide Metabolism isa 90001 0 0 0 80 Amino Acid Metabolis
83. gle command line n node attrs lt file gt This option specifies a node attributes file You may specify as many node attribute files as desired on a single command line m matrix lt file gt This option specifies a data matrix file In a biological context the data matrix consists of expression data All data matrix files are read into node attributes You may specify as many data matrix files as desired on a single command line p plugin lt file gt This option specifies a cytoscape plugin jar file to be loaded by Cytoscape This option also subsumes the previous resource plugin option You may specify a class name that identifies your plugin and the plugin will be loaded if the plugin is in Cytoscape s CLASSPATH For example assuming that the class MyPlugin can be found in the CLASSPATH you could specify the plugin like this cyto scape sh p MyPlugin class A final means of specifying plugins is to specify a file name whose contents contain a list of plugin jar files P props lt file gt This option specifies Cytoscape properties Properties can be specified either as a properties file in Java s standard properties format or as individual properties To specify individual properties you must specify the property name followed by the property value where the name and value are separated by the sign For ex ample to specify the defaultSpeciesName cytoscape sh P defaultSpeciesName Human If you would like to inclu
84. gorithm can be applied to the entire network or a portion of it by selecting the appropriate options from Layout Cytoscape Layouts Spring Embedded A sample screen shot is provided below eA A sample em _ Sa T ar EN het I tee a p 2 A z jut gaje a ie yny a a a k z iy p a ret hh Aa ei z S d i a O sei han SS A E S 11 m iny om 7e n ot a shee yFiles Circular Layout This algorithm produces layouts that emphasize group and tree structures within a network It partitions the network by analyzing its connectivity structure and arranges the partitions as separate circles The circles themselves are arranged in a radial tree layout fashion This algorithm is available by selecting Layout yFiles Circular 37 Cytoscape User Manual yFiles Hierarchical Layout The hierarchical layout algorithm is good for representing main direction or flow within a network Nodes are placed in hierarchically arranged layers and the ordering of the nodes within each layer is chosen in such a way that minimizes the number of edge crossings This algorithm is available by selecting Layout yFiles Hierarchical yFiles Organic Layout The organic layout algorithm is a kind of spring embedded algorithm that combines elements of the other algorithms to show the clustered structure of a graph This algorithm is available by selecting Layout gt yFiles Organic 3
85. gradient Step 1 Load a sample network From the main menu select File Import gt Network Multiple file types and select sampleData galFiltered sif Step 2 Load sample expression data From the main menu select File Import Attribute Expression Matrix and select sampleData galExpData pvals Step 3 Open the VizMapper Select the View Open VizMapper menu option or select the VizMapper icon in the main button bar or click on the VizMapper tab in the Control Panel at the left of the screen Step 4 Create a new visual style Click the Options button and select Create new visual style Name your new style Tutorial VS3 Step 5 Choose a visual attribute Double click the Node Color entry listed in Unused Properties Node Color will now appear at the top of the list under the Node Visual Mapping category Step 6 Choose a network attribute Click on the cell to the right of the Node Color entry and select gallRGexp from the dropdown list that appears Step 7 Choose a mapping type Set the Continuous Mapping option as the Mapping Type Step 8 Define the points where colors will change Double click on the white rectangle next to Graph ical View to open the Color Gradient Mapper Click the Add button twice to create two data points which will show up as overlapping triangles at the right of the scale Click and drag one point to 1 or type the value in the Range Setting box Set the second point to
86. he file contains no tabs then any spaces are delimiters that separate names and names cannot contain spaces If your network unexpectedly contains no edges and node names that look like edge names it probably means your file contains a stray tab that s fooling the parser On the other hand if your network has nodes whose names are half of a full name then you probably meant to use tabs to separate node names with spaces Networks in simple interactions format are often stored in files with a sif extension and Cytoscape recog nizes this extension when browsing a directory for files of this type GML Format In contrast to SIF GML is a rich graph format language supported by many other network visualization packages The GML file format specification is available at http www infosun fm1 uni passau de Graphlet GML It is generally not necessary to modify the content of a GML file directly Once a network is built in SIF format and then laid out the layout is preserved by saving to and loading from GML Visual attributes specified in a GML file will result in a new visual style named Filename style when that GML file is loaded XGMML Format XGMML is the XML evolution of GML and is based on the GML definition In addition to network data XGMML contains node edge network attributes The XGMML file format specification is available at http www cs rpi edu puninj XGMML XGMML is now preferred to GML because it offers the flexibi
87. hem will change Cytoscape s default memory parameters except starting from the command line Option A Command line startup note this does not permanently change Cytoscape s default 512M setting If you are opening Cytoscape from the command line using the command e java Xmx512M jar cytoscape jar p plugins then you can increase the value of Xmx to the desired amount of memory For example e java Xmx800M jar cytoscape jar p plugins Option B Using cytoscape bat Windows systems 1 Open the file cytoscape bat in a text editor eg right click and select Open With Notepad 2 Increase the value of the Xmx tag found in the last line of the file as per Option A Do not modify other parts of the file 3 Save and close the file 4 Open Cytoscape by double clicking on cytoscape bat Option C Using cytoscape sh UNIX Linux and Mac OS X systems 1 Open the file cytoscape sh in a text editor eg right click and select Open With TextEdit 118 oF 4 Cytoscape User Manual Increase the value of the Xmx tag found in the last line of the file as per Option A Do not modify other parts of the file Save and close the file Open Cytoscape by running cytoscape sh from the command line Option D Using the Cytoscape icon Mac OS X systems l 2 3 4 gt In the Finder right click on the Cytoscape icon and select Show Package Contents Go to the Contents folder and open the file info p
88. hing node Cytoscape will automatically zoom in on the selected node 76 Cytoscape User Manual a default HA Search galFiltered sif Configuring Quick Find Quick Find works by creating an internal index of all nodes within the network By default Cytoscape indexes all nodes by the node identifier However you can configure Quick Find to index nodes or edges and you can set any attribute as the index For example if you load up a BioPAX file such as sampleData Apoptosis_BioPAX xml your network will be automatically annotated with numerous attributes To index the network based on cellular location click the Quick Find configuration button and select biopax cellular_location from the dropdown list 809A Configure Search Options for Apoptosis Select Index Type Index Nodes Index Edges Select Attribute Search on Attribute biopax cellular_location HA Attribute Description A list of one or more cellular locations e g cytoplasm This attribute should reference a term in the Gene Ontology Cellular Component ontology Sample Attribute Values extracellular region plasma membrane mitochondrial outer membrane cytosol mitochondrial intermembrane space Reindex Network A Woe You can then quickly find all proteins located in the plasma membrane by just typing p 77 Cytoscape User Manual BioPAX v 0_5 Tip If you don t know what to search for just leave the sear
89. ibute using the dropdown list provided Complex attributes such as lists are not supported Key Attribute for Network pleno _ _ _ v dp annotation Taxon dy annotation Ob Object_Name dp canonicalNam e Cytoscape uses a simple mechanism to manage aliases of objects Both nodes and edges can have aliases If an attribute is loaded as an alias it is treated as a special attribute called alias This will be used when mapping attributes If the primary key and key attribute for an object do not match Cytoscape will search for a match between aliases and the key attribute To define an alias column in the attribute table just click on the checkboxes to the left of the column name while importing 31 Cytoscape User Manual Alias Column Attribute Name Data Type Column 1 ih String Column 2 dp String E Column 3 dp String Column 4 b Float Column b Float Text File Import Options For more detail on these options please see the Import Free Format Table Files section of the user manual in the Creating Networks chapter Attribute Browser Cyioranel iD annotation 2O BhOLOCICAL_ PROCESS annotation DB_Object_Name YOL128C protein amino acid phosphorfation protein kinase 5000005486 TGK3 protein YGR253C response to stress sporulation sen proteasome subunit DO45 PUP2Z 3000003485 YDL230W protein amino acid d phosphor dati phosphotyrosine specific pr PTF 1 30000022839 ph
90. ically saved with the session they were created in Before Cytoscape exits you will be prompted to make sure you save the session before quitting It is also possible to save your visual styles in a file separate from the session file To do this navigate to the File gt Export Vizmap Property File menu option and save the properties as a file This feature can be used to share visual styles with other users Importing Visual Styles To import existing visual styles navigate to the File Import gt Vizmap Property File menu option and select a vizmap props file Imported properties will supplement existing properties or override existing properties if the properties have the same name You can also specify a visual properties file using the V command line option cytoscape sh V myVizmap props Visual properties loaded from the command line will override any default properties Default Visual Styles It is possible to change the default visual properties for all sessions of Cytoscape To do this navigate to the Edit Preferences Properties menu option check the Make Current Visual Styles Default box in the Default Visual Styles section and click the OK button This will save the current visual styles as a vizmap props file to your cytoscape directory found in your home directory These visual styles will then be loaded each time Cytoscape is started 74 Cytoscape User Manual Bypassing Visual Styles Cytoscape
91. ider No Graient 2 Sliders Continuous Continuous Editor 609A Continuous Editor for Node Size rContinuous Mapping for Node Size F F Node Size 5 0000 10 0000 Degree Max 18 0 Range Setting 10 Add Delete Continuous Continuous Editor is for creating mapping between numerical attributes and numerical visual properties size opacity To change the value assigned on Y axis visual property shown in the example above is node size drag the red squares or double click on the squares to directly type exact value 73 Cytoscape User Manual Continuous Discrete Editor 9089 Continuous Editor for Node Shape Continuous Mapping for Node Shape Min 1 0 4 97196 1247897 _ggs74s Degree Range Setting 4 972 5 Add Delete Continuous Discrete Editor is used to create mapping from numerical attribute values to discrete visual properties such as font shape or line style To edit a value for specific region double click on the icon on the track Managing Visual Styles All Cytoscape Visual Style settings are initially loaded from a a default file called vizmap props that cannot be altered by users When users make changes to the visual properties a vizmap props file is saved in the session file This means that assuming you save your session you will not lose your visual properties No other vizmap props files are saved during normal operation Saving Visual Styles Visual styles are automat
92. if 2 Apply layout to the network From the main menu select Layout gt Cytoscape Layouts Degree Sorted Circle Layout This layout algorithm sort nodes in a circle by degree of the nodes Degrees will be stored as node attribute names Degree after you applied this algorithm 3C 1 1 c k t h e Vi z M a p O e button on the tool bar 4 Click Defaults panel on the VizMapper main panel Default Apearence Editor pops up see below 5 Edit the following visual properties and press Apply Since you changed opacity of the node you can see the nodes bihind the front node see below e Node Oppacity 100 e Edge Color White e Background Color Black 67 Cytoscape User Manual 8Ae Cytoscape Desktop New Session EUa pag is Cortrol Pare fal ADA galFiltered sif i Network VieMapper Editor b i Curent Visaal Style wn P G Defaults Visual Mapping browser a E T Mode Visual Map E Node Label ci F Unused Properties Hode Color Node Border Color Node Shape Mode Sine Node Width Hode pitii Hode Font Face Hode Font Sze Node Lake Cater Node Tania Node Label Position Welcome b Lyipecapp 2 5 Hgnt click drag te ULIM Middla clitk drag to PAN 6 Cretate a Discrete Node Color Mapping Select Degree as controlling attribute 7 Select Node Color then right click to show popup menu Select Generate discrete values gt Rainbow 1 It generates different colors for different attrib
93. in jar file directory of jar files plugin class name or plugin jar URL P props lt file gt Load cytoscape properties file Java properties format or individual property P name value V vizmap lt file gt Load vizmap properties file Java properties format Any file specified for an option may be specified as either a path or as a URL For example you can specify a network as a file assuming that myNet sif exists in the current working directory cytoscape sh N myNet sif Or you can specify a network as a URL cytoscape sh N http example com myNet sif 14 Cytoscape User Manual Table 7 h help This flag generates the help output you see above and exits v version This flag prints the version number of Cytoscape and exits s session lt file gt This option specifies a session file to be loaded Since only one session file can be loaded at a given time this option may only specified once on a given command line The option expects a cys Cytoscape session file It is customary although not necessary for session file names to contain the cys extension N network lt file gt This option is used to load all types of network files SIF GML and XGMML files can all be loaded using the N option You can specify as many networks as desired on a single command line e edge attrs lt file gt This option specifies an edge attributes file You may specify as many edge attribute files as desired on a sin
94. ing system The Network Overview Window The network overview window shows an overview or bird s eye view of the network It can be used to navigate around a large network view The blue rectangle indicates the portion of the network currently 13 Cytoscape User Manual displayed in the network view window and it can be dragged with the mouse to view other portions of the network Zooming in will cause the rectangle to appear smaller and vice versa e Li Moni Cees Ca Genie bell cps ms sy a fay i n tok G ad E kp a SZ Ta irp haw Ar P a A a N T Di maei Weka pia Pr 7 oe nis p HD Pa mapp krepi Overview Network View Command Line Arguments Cytoscape recognizes a number of optional command line arguments including run time specification of network files attribute files and session files This is the output generated when the cytoscape is executed with the h or help flag usage java Xmx512M jar cytoscape jar OPTIONS h help Print this message v version Print the version number s session lt file gt Load a cytoscape session cys file N network lt file gt Load a network file any format e edge attrs lt file gt Load an edge attributes file edge attribute format n node attrs lt file gt Load a node attributes file node attribute format m matrix lt file gt Load a node attribute matrix file table p plugin lt file gt Load a plug
95. ion the value here will be used as the interaction type for all edges Modify Attribute Name Type Set AtnibUTe Name and Type Attribute Name and Type Attribute name for Column 5 entry Attribute Data Type String Integer Floating Point C Boolean 4 List List Delimiter is Attribute names and data types can be modified here 22 Cytoscape User Manual e Modify Attribute Name just enter a new attribute name and click OK e Modify Attribute Data Type The following attribute data types are supported e String e Boolean True False e Integer e Floating Point e List of one of String Boolean Integer Floating Point Cytoscape has a basic data type detection function that automatically suggests the attribute data type of a column according to its entries This can be overridden by selecting the appropriate data type from the radio buttons provided For lists a global delimiter must be specified 1 e all cells in the table must use the same delimiter Edit a New Network A new empty network can also be created and nodes and edges manually added To create an empty network go to File New gt Network Empty Network and then manually add network components using the Editor in CytoPanel 1 see the Editor chapter for more details Supported Network File Formats Cytoscape can read network pathway files written in the following formats e Simple interaction file SIF or sif format e Graph Markup L
96. is example starts with the letters SP See the README file for more information ftp ftp ebi ac uk pub databases GO goa HUMAN README Finally run the script to create your three annotation files for human proteins 109 Cytoscape User Manual e bioproc anno GO biological process annotation e molfunc anno GO molecular function annotation e cellcomp anno GO cellular component annotation using the supplied python script It may be necessary to modify this script slightly if RefSeq identifiers are not used as canonical names or if you are using a more recent version of Python python parseAssignmentsToFlatFileFromGoaProject py gene_association goa_human xrefs goa See below for Python script listing Python script examples These scripts as described above require Python version 2 2 or later Script 1 parseGoTermsToFlatFile py parseGoTermToFlatFile py translate a GO XML ontology file into a simpler Cytoscape flat file RCS Revision 1 3 Date 2003 05 18 00 38 43 def flatFilePrint id name isaIDs partofIDs isa if len isaIDs gt 0 isa isa for isaID in isaIDs isa isaID isa t An isa partof if len partofIDs gt 0 partof partof for partofID in partofIDs partof partofID partof t partof t result np np s np np s np np s np np s np np id name isa partof result result strip if result isa isa o
97. is not the intent of this section to claim rights or contest your rights to work written entirely by you rather the intent is to exercise the right to control the distribution of derivative or collective works based on the Library In addition mere aggregation of another work not based on the Library with the Library or with a work based on the Library on a volume of a storage or distribution medium does not bring the other work under the scope of this License 3 You may opt to apply the terms of the ordinary GNU General Public License instead of this License to a given copy of the Library To do this you must alter all the notices that refer to this License so that they refer to the ordinary GNU General Public License version 2 instead of to this License If a newer version than version 2 of the ordinary GNU General Public License has appeared then you can specify that version instead if you wish Do not make any other change in these notices Once this change is made in a given copy it is irreversible for that copy so the ordinary GNU General Public License applies to all subsequent copies and derivative works made from that copy This option is useful when you wish to copy part of the code of the Library into a program that is not a library 4 You may copy and distribute the Library or a portion or derivative of it under Section 2 in object code or executable form under the terms of Sections and 2 above provided that you accompan
98. l links are specified in a linkout props file which is included in the cytoscape jar file The defaults include a number of links such as Entrez SGD 1HOP and Google as well as a number of species specific links In addition to the default links users can customize the LinkOut menu by adding or removing links by editing the linkout properties found under Edit Preferences Properties External links are listed as key value pairs in the linkout props file where key specifies the name of the link and value is the search URL The LinkOut menus are organized in a hierarchical structure that is specified in the key All key terms start with the keyword linkouturl For example the following entry linkouturl yeast SGD http db yeastgenome org cgi bin locus pl locus 1D places the SGD link under the yeast submenu This link will appear in Cytoscape as Visual Mapping Bypass LinkQut Entrez b Biological resources Reactome b Web resources IHOP BiotsRID OFT human b i i i Fly d UniProt b moJsSE In a similar fashion one can added new submenus The ID string in the URL is a place holder for the node label When the popup menu is generated this marker is substituted with the node label In the above example the generated SGD link for the YIM1 protein is http db yeastgenome org cgi bin locus pl locus YIM1 If you want to query based on a different attribute you currently need
99. le menu contains most basic file functionality File gt Open for opening a Cytoscape session file File New for creating a new network either blank for editing or from an existing network File Save for saving a session file File Import for importing data such as networks and attributes and File gt Export for exporting data and images Also File Print allows printing while File Quit closes all windows of Cytoscape and exits the program OG Edt view se j New I Open O Save S Save As 5 Import e Export gt Print a Quit gQ Edit The Edit menu contains Undo and Redo functions which undo and redo edits made in the Attribute Browser the Network Editor and to layout There are also options for creating and destroying views graphical representations of a network and net works the raw network data not yet visualized as well as an option for deleting selected nodes and 10 Cytoscape User Manual edges from the current network All deleted nodes and edges can be restored to the network via Edit gt Undo Editing preferences for properties and plugins is found under Edit Preferences Properties j Edit View Select Layout Plugins Undo Move zi i Destroy View AW I Destroy Network TW Preferences p View The View menu allows you to display or hide the network management panel CytoPanel 1 the attribute browser CytoPanel 2 the Network Ove
100. list In the Property List Editor expand the Root directory then Java and modify the VMOptions value originally set as Xmx512M as per Option A Do not modify other parts of the file Save and close the file Open Cytoscape by double clicking on the icon Option E Using the Cytoscape icon Windows systems 1 2 Open the file cytoscape lax in a text editor Increase the numerical value bytes of memory of the heap size and stack size lines shown below at 800M e lax nl java option java heap size max 838860800 lax nl java option native stack size max 838860800 Do not modify other parts of the file and be careful not to add any trailing spaces to these lines Save and close the file Open Cytoscape by double clicking on the icon 119
101. lity associated with all XML document types If you re unsure about which to use choose XGMML SBML Systems Biology Markup Language Format The Systems Biology Markup Language SBML is an XML format to describe biochemical networks SBML file format specification is available at http sbml org documents BioPAX Biological PAthways eXchange Format BioPAX is an OWL Web Ontology Language document designed to exchange biological pathways data The complete set of documents for this format is available at http www biopax org index html 25 Cytoscape User Manual PSI MI Format The PSI MI format is a data exchange format for protein protein interactions It is an XML format used to describe PPI and associated data PSI MI XML format specification is available at http psidev sourceforge net mi xml doc user Delimited Text Table and Excel Workbook Cytoscape has native support for Microsoft Excel files xls and delimited text files The tables in these files can have network data and edge attributes Users can specify columns containg source nodes target nodes interaction types and edge attributes during file import For more detail please read the Import Free Format Tables section section of the Creating Networks chapter Node Naming Issues in Cytoscape Typically genes are represented by nodes and interactions or other biological relationships are represented by edges between nodes For compactness a gene al
102. llow selection based on the application of pre existing filters e Topology filters allow selection of nodes with neighbors that match some pre existing filter e Boolean filters allow the combination of multiple filters using the AND OR and XOR operators Example filters are shipped with the plugin to get started To use the old filters go to Select Use Old Filters You will see a filters window which initially looks like the following Use Filters Manage Filters There is no filter currently selected To edit a Filter select it from the Available Create new filter Remc ted Filte filters list IF the list is empty you can create a new Filter with the Create new Available Filters Filter button Select All Filter Node canonicalName YL Node canonicalName C If the first filter is selected then the window looks as shown Use Filters Manage Filters String Pattern Filter Create new Filter Remove selected Filter Available Filters Filter Nare e canonicalName YL Select All Filter Node canonicalName YL 0 Select graph objects of type Node Node canonicalName YC i with a value For text attribute canonicalName that matches the pattern L Apply selected Filter There are three panels in the Filters window e The right hand panel An existing or newly created filter can be edited in this area Each filter type has its
103. ltered sif Step 2 Open the VizMapper Select the View Open VizMapper menu option or select the VizMapper icon in the main button bar or click on the VizMapper tab in the Control Panel at the left of the screen Step 3 Create a new visual style Click the Options button and select Create new visual style Name your new style Tutorial VS2 Step 4 Choose a visual attribute Double click the Edge Color entry listed in Unused Properties Edge Color will now appear at the top of the list under the Edge Visual Mapping category as shown below 63 Cytoscape User Manual Visual Mapping Browser Edge Color Please select an attribute Mapping Type Y Unused Properties Feine Fant Fare Manha lirke ta rreate Step 5 Choose a network attribute Click on the cell to the right of the Edge Color entry and select in teraction from the dropdown list that appears Step 6 Choose a mapping type Set the Discrete Mapper option as the Mapping Type All available at tribute values for interaction will be displayed as shown below Y Edge Visual Mapping Edge Color interaction Mapping Type Discrete Mapping pd pp Step 7 Set the mapping relationship Click the empty cell next to pd protein DNA interactions On the right side of the cell and X buttons will appear Click on the button A popup window will appear select blue and the change will immediately appear on the network wind
104. m isa 90001 80 etabolism of Other Amino Acids isa 90001 80 etabolism of Complex Carbohydrates isa 90001 01 03 02 04 05 06 07 The format has these required features e The first line contains two parenthesized assignments for curator and type In the GO example above the ontology file which is created from the XML that GO provides nests all three specific ontologies molecular function biological process cellular component below the root ontology named Gene_Ontology type all tells you that all three ontologies are included in that file e Following the mandatory title line there are one or more category lines each with the form e number0 name 1isa partof numberl number2 where isa and partof are terms used in GO they describe the relation between parent and child terms in the ontology hierarchy e The trailing blank before each left square bracket is not required it is an artifact of the python script that creates these files The Annotation Format By example from the GO biological process annotation file species Saccharomyces cerevisiae type Biological Process curator GO0 YMRO56C 0006854 YBRO85W 0006854 YJR155W 0006081 and from KEGG species Mycobacterium tuberculosis type Metabolic Pathways curator KEGG RVO761C 10 RVO761C 71 RVO761C 120 RVO761C 350 RVO7T61C 561 RV1862 10 The format has these required features e The fi
105. meric indices in the same manner as that of Quick Find 81 Cytoscape User Manual Note that by default the filter will apply the AND relationship if multiple attributes are defined In the previous figure the filter will select all the nodes edges whose Annotation Date contains the pattern 2000 and whose gal1RGsig value falls within the defined range In Cytoscape 2 5 only the AND and OR relationships can be used Other Boolean operations XOR and NOT are not yet available The OR re lationship can be selected from the advanced options panel see below Advanced Options The Advanced panel can be opened by clicking on the plus sign It looks like this Save Session _ Global Select Node Edge Edge Source w Target Relation AND O OR There are four rows in the advanced panel 1 The first row labeled Save The two checkboxes Global and Session will determine where the filter is saved By default filters are saved in individual sessions By checking the Global checkbox the filter will be saved in the global properties file Note also that the prefix of the filter name in the Current Filter dropdown list will reflect where it is saved 2 The second row labeled Select will determine whether the filter will select network nodes edges or both If Node is checked Edge is unchecked then only nodes will be considered for selection not edges Note also that the attributes listed in the Attribute dropdow
106. n Cytoscape 2 3 a new network rendering engine is being introduced The goal of the rendering engine is to be able to display large networks gt 10 000 nodes yet retain interactive speed To accomplish this goal a technique involving level of detail LOD is being used Based on the number of objects nodes and edges being rendered an appropriate level of detail is chosen For example by default node labels if present are only rendered when less than 100 nodes are visible because drawing text is a relatively expensive operation This can create some unusual behavior If the screen currently contains 98 nodes node labels will be displayed If you pan across the network such that now 101 nodes are displayed the node labels will disappear As another example if the sum of rendered edges and rendered nodes is greater than or equal to a default value of 2000 a very coarse level of detail is chosen where edges are always straight lines nodes are always rectangles and no antialiasing is done The default values used to determine these thresholds can be changed by setting properties under Edit Preferences Properties Low LOD vs High LOD Table 25 Large Network with Low LOD _ Large Network with High LOD With low LOD values all nodes are displayed as square and anti alias is turned off With high LOD values anti alias is turned on and nodes are displayed as actual shape user specified in the Visual Style Parameters for Cont
107. n Tie Spale eeternal bo Che gufernmst siruciure af accel For ces aio sxian projeti oe exer encapsulating siruciure GOGRS557S sxiracelidar marik angi he We laar CONG maniy af prasine dapeialy Collagen and ghroraminoghaans mipi as Pro ete yo ana Par temi a as GOhKOO0S415 esiracelular space Tha part of amahicelular organem aide the cells proper usudi iaken to be midde the pasma membranes and orup h CCeOb0S518 cell wall The rigid or s4mi rigd emalii heng guiside ihe el memorane of Glan lungel and moil pikana Ces mounening her GO O00562 2 inraceiluar The ihig comers ofa cali ihe marter conidia wihikan Gun no uding the plasma mamira Gali taken 10 ached lar COhRORDShI3 cel The basi siruciural and funcional uni of all organisms Includes ihe plasma membrane aed ary eternal encapsulating siruci CO0 SSI 4 nucle 4 membrine Diundad ggarsjie of akanai oes in which chroigmes are Paused and repika a maa cely ma purje G DHS G35 nuclear anwhps The dobia lipii bimar erclosing the nucleus awd separating itt comente Trem the rast of the Caoplatn includes ea imema GELDES S4 nuclesplasm Tha part of the mules conten oiher an ihe throamasaomes or ihe sucledus TE _ d Fim ra i i a T 4 ities d Mode Annbine roaser Edge Anribuie rower Network Atnribure Browser e Note 1 Some ontologies have a lot of terms For example the full Gene Ontology contains more than 20 000 terms If you need to save memory you can remove this o
108. n chosen creates a clique amongst the selected nodes The editor provides accelerators for adding nodes and edges Control clicking at a position on the canvas creates a node at that position The NODE_TYPE attribute of the node will be the same as the NODE_TY PE of the node most recently added defaulting back to the original visual style In this manner you can use control clicking as a kind of stamp to add multiple nodes of the same type to the network Control clicking on a node on the canvas starts an edge with its source at that node Move the cursor and a rubber banded line will follow the cursor As the cursor passes over another node that node is highlighted and the rubber banded line will snap to a connection point on that second node Control click the mouse again and the connection will be established The EDGE_TYPE attribute of the edge will be the same as the EDGE_TYPE of the edge most recently added defaulting back to the original visual style You can abort the drawing of the edge by control clicking on an empty spot on the palette You can delete nodes and edges by selecting a number of nodes and edges then selecting Edit Delete Selected Nodes and Edges You can recover any nodes and edges deleted from a network by going to Edit Undo However note that this will restore all nodes and edges that were previously deleted from the network not just those deleted by the most recent delete operation 88 Cytoscape User Manu
109. n list will be only those with prefix node 3 The third row edge will determine either Source or Target nodes will be selected since there is a dis tinction between source nodes and target nodes in a directed network 4 The last row Relation will determine what boolean operation will be applied to each individual widget atomic filter For the time being there are only tow options AND and OR More boolean operations will be added in the future versions If you need to do complex selection please use the old filters below Modifying Filters The Option button at the right of the Current Filter contains a few functionalities other than creating new filters e Delete filter this will delete the selected filter e Rename filter this will give user the option to change the name of the selected filter e Copy existing filter this will duplicate the selected filter Using Old Filters The old filters is the one existed in previous versions of Cytoscape Several types of filters are available Basic filters allow the selection of multiple nodes or edges according to singe attribute data e String filters allow selection of nodes or edges with attributes matching specified text patterns These patterns may include the wildcards and 82 Cytoscape User Manual e Numerical filters allow selection of nodes or edges according to numerical attributes and the mathemat ical operators gt and lt Compound filters a
110. nated place offer equivalent access to copy the above specified materials from the same place e Verify that the user has already received a copy of these materials or that you have already sent this user a copy 115 Cytoscape User Manual For an executable the required form of the work that uses the Library must include any data and utility programs needed for reproducing the executable from it However as a special exception the materials to be distributed need not include anything that is normally distributed in either source or binary form with the major components compiler kernel and so on of the operating system on which the executable runs unless that component itself accompanies the executable It may happen that this requirement contradicts the license restrictions of other proprietary libraries that do not normally accompany the operating system Such a contradiction means you cannot use both them and the Library together in an executable that you distribute 7 You may place library facilities that are a work based on the Library side by side in a single library to gether with other library facilities not covered by this License and distribute such a combined library provided that the separate distribution of the work based on the Library and of the other library facilities is otherwise permitted and provided that you do these two things a Accompany the combined library with a copy of the same work based on the Lib
111. nd size number of nodes and edges which are shown in the network manager If a network is loaded from a file the network name is the name of the file Some networks are very large thousands of nodes and edges and can take a long time to display For this reason a network in Cytoscape may not contain a view Networks that have a view are highlighted in green and networks that don t have a view are highlighted in red You can create or destroy a view for a network by right clicking the network name in the network manager or by choosing the appropriate option in the Edit menu You can also destroy previously loaded networks this way In the picture above seven networks are loaded six green ones with views and one red one without a view Certain operations in Cytoscape will create new networks If a new network is created from an old network for example by selecting a set of nodes in one network and copying these nodes to a new network via the File New Network option it will be shown as a child of the network that it was derived from In this way the relationships between networks that are loaded in Cytoscape can be seen at a glance Networks in the top part of the tree in the figure above were generated in this manner The available network views are also arranged as multiple overlapping windows in the network view window You can maximize minimize and destroy network views by using the normal window controls for your operat
112. ned to cut down on the number of pop up windows within Cytoscape and to create a more unified user experience These panels used to be called CytoPanel 1 2 and 3 From 2 5 they are named based on their functions The following screenshot shows the file yeastHighQuality sif and GO annotations loaded into Cytoscape performed Force Directed layout enable 90 Cytoscape User Manual Align and Distribute tools and then run MCODE plugin for the data sets In Control Panel at the left hand side of the screen the Network Manager Network Overview VizMapper Filters and Cytoscape Editor have been loaded On the bottom of the panel there is another CytoPanel called Tool Panel In the Data Panel the Attribute Browser has been loaded In addition Result of the analysis by MCODE plugin is Shown in Result Panel at the right hand side eee Spaai pppn Carral Fane a Ty Network VaMapper iior Curctat Visual dye _ a A irfist Vitwal Magping Browser T heeds Wied Mare irng al aoe Filner KF T kiip Codes eae n aa Massing Tyt Cai Mapag Craan ira EB T hafe tape MAOGA Meje Sami Rani Tete Berit Aiha ag Duan ture ted L ster Ucina 3 DONO T Leer Piiri padt Betder Cie made bt Tog Fare a acetates Del i Rene Cvicncape Desiion Gertie janes tho cya weet ht uaiti arein Ci PM Cele Pe Bask 8 bite tas feta Di Hagen 216 Biak ETE 2 Peter 10 ee Dissi bid miai iil C
113. ns either of that version or of any later version published by the Free Software Foundation If the Library does not specify a license version number you may choose any version ever published by the Free Software Foundation 14 If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible with these write to the author to ask for permission For software which is copyrighted by the Free Software Foundation write to the Free Software Foundation we sometimes make exceptions for this Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally NO WARRANTY 15 BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE THERE IS NO WARRANTY FOR THE LIBRARY TO THE EXTENT PERMITTED BY APPLICABLE LAW EXCEPT WHEN OTHER WISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR OTHER PARTIES PROVIDE THE LIBRARY AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE LIBRARY IS WITH YOU SHOULD THE LIBRARY PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION 16 INNO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER OR ANY OTHER PARTY WHO MAY MODIFY A
114. ntenance of the structure and integrity of the mitochondrial genome GOC ai is_a GO 0007005 mitochondrion organization and biogenesis Default List of Ontologies Cytoscape provides a list of ontologies available in OBO format If an Internet connection is available Cytoscape will import ontology and annotation files directly from the remote source The table below lists the included ontologies 95 Cytoscape User Manual Table 27 Gene Ontology Full This data source contains a full size GO DAG which contains all GO terms This OBO file is written in version 1 2 format Generic GO slim A subset of general GO Terms including higer level terms only Yeast GO slim A subset of GO Terms for annotating Yeast data sets maintained by SGD Molecule role INOH Pro A structured controlled vocabulary of concrete and abstract generic protein tein name family name on names This ontology is a INOH pathway annotation ontology one of a set tology of ontologies intended to be used in pathway data annotation to ease data in tegration This ontology is used to annotate protein names protein family names and generic concrete protein names in the INOH pathway data INOH is part of the BioPAX working group Event INOH pathway onto A structured controlled vocabulary of pathway centric biological processes logy This ontology is a INOH pathway annotation ontology one of a set of onto logies intended to be used in pathway data annotation to
115. ntology DAG from Network Panel right click on the ontology name at the left hand side of the screen and select Destroy Network e Note 2 All ontology DAGs will be saved in the session file To minimize the session file size you can delete the Ontology DAG before saving session Gene Association File The Gene Association GA file provides annotation only for the Gene Ontology It is a species specific annotation file for GO terms Gene Association files will only work with Gene Ontologies and NOT others Sample Gene Association File gene_association sgd annotation file for yeast SGD 5000003916 AAD10 GO 0006081 SGD_REF S000042151 PMID 10572264 ISS P aryl alcohol dehydrogenase putative YJR155W gene taxon 4932 SGD S000005275 AADI4 GO 0008372 SGD_REF 5000069584 ND aryl alcohol dehydrogenase putative YNL331C gene taxon 4932 20010119 97 Cytoscape User Manual Node Name Mapping If you have a network file and an attribute file they should have a common key to map attributes onto network data If those two do not have a common key you need to do an extra step to add a shared key The following is a quick tutorial to learn how to use Gene Name Mapping files Import Network and Name Mapping Files 1 Download name mapping files Mapping files are available at http chianti ucsd edu kono genenamemap ping html In this tutorial we are going to use dictionary_no_prefix zip which is a file set without prefixes for each gene
116. oPanel 5 Rotate Scale Scale a lt j l 1 8 1 4 1 2 1 2 4 8 Vv Scale Selected Nodes Only After AAA sample CytoPanel 5 Rotate 41 Cytoscape User Manual Align Distribute Stack ie Align ES soe ae g Distribute bb Toe a ESEN gt Stack alalar itik N Selecting the Layout Align Distribute option will open the Align Distribute Stack window in CytoPanel 5 The Align buttons provide different options for either vertically or horizontally aligning selected nodes against a line The differences are in what part of the node gets aligned e g the center of the node the top of the node the left side of the node The Distribute buttons evenly distribute selected nodes between the two most distant nodes along either the vertical or horizontal axis The differences are again a function what part of the node is used as a reference point for the distribution And the Stack buttons vertically or horizontally stack selected nodes with the full complement of alignment options The table below provides a decription of what each button does Table 13 Description of Align Options Vertical Align Top The tops of the selected nodes are aligned with the top most node Vertical Align Center The centers of the selected nodes are aligned along a line defined
117. ode nd Welcome to Cytoscape 2 5 Right click drag to ZOOM Middle click drag to PAN To edit an existing network just select the Editor tab in CytoPanel 1 To start editing a new network create a new network by going to File New Network Empty Network To add a node to a network drag and drop a node shape from the palette onto the canvas To connect two nodes with an edge drag and drop an arrow shape onto a node on the canvas This node becomes the source node of the edge Move the cursor and a rubber banded line will follow the cursor As the cursor passes over another node that node is highlighted and the rubber banded line will snap to a connection point on that second node Click the mouse while over this node and the connection will be established 87 Cytoscape User Manual a Cytoscape Version 2 5 File Edit View Select Layout Plugins Help e666 Cytoscape Desktop New Session A E 7 jaEGQQgaagags Control Panel va OOH Network 0 is Network VizMapper Editor Filters Directed Edge Add a Node _ wa Welcome to Cytoscape 2 5 Right click drag to ZOOM Middle click drag to PAN You can abort the drawing of the edge by clicking on an empty spot on the palette Note that if you change the Visual Style the palette used by the current network view will also change to be consistent with the mappings in the new Visual Style There is also an Edit gt Connect Selected Nodes option that whe
118. ode or can get it if you want it that you can change the software and use pieces of it in new free programs and that you are informed that you can do these things To protect your rights we need to make restrictions that forbid distributors to deny you these rights or to ask you to surrender these rights These restrictions translate to certain responsibilities for you if you dis tribute copies of the library or if you modify it For example if you distribute copies of the library whether gratis or for a fee you must give the recipients all the rights that we gave you You must make sure that they too receive or can get the source code If you link other code with the library you must provide complete object files to the recipients so that they can relink them with the library after making changes to the library and recompiling it And you must show them these terms so they know their rights We protect your rights with a two step method 1 we copyright the library and 2 we offer you this license which gives you legal permission to copy distribute and or modify the library To protect each distributor we want to make it very clear that there is no warranty for the free library Also if the library is modified by someone else and passed on the recipients should know that what they have is not the original version so that the original author s reputation will not be affected by problems that might be introduced by others Finally
119. odes and an optional edge interaction type 19 Cytoscape User Manual INGOT NEWO Bnd Edge ATInOULeSs Mam fable Import Network from Table Data Sources Input File file cellar users kono workspace cytoscape testData galFiltered xls Select File Interaction Definition Source Interaction Interaction Type Target Interaction Column 1 amp gt eb Column2 x O Columns in BLUE will be loaded as EDGE ATTRIBUTES Arwanc ea Show Text File import Options Preview Excel Workbook Left Click Edit Column Right Click ON OFF Column Yeast Network Sheet 1 W Column 1 2 Column 2 amp Column 3 Boolean At amp Text Attr 1 X Column amp Y KRROZ6C GLI2Z2C fal se abcd 12345 1 2344543 a YTGR2 18W YGLOI7W true abcd1 346 127344543 E YGLO97W YOR 04W true abcd12347 12344543 YLR249W YPROSOW true abcd 1 348 1 2344543 YLR2 49W YER118W true abcd1 349 1 2344543 YLR293C YGLO97W true abcd12350 1 2344543 Y MR146C YDR429C pr true abcd12351 12344543 YDR429C YFLOI7C true abcd12352 1 2344543 YPROSOW YALOOSW py true abcd 12353 12344543 es ee ee ee ee eS mhe oa C E ee ee a e Cancel Supported Files The Import Network from Table function supports delimited text files and single sheet Microsoft Excel Workbooks The following is a sample table file source target interaction boolean attribute string attri
120. of California at San Francisco ji Funding for Cytoscape is provided by a federal grant from the U S National Institute of General Medical Sciences NIGMS of the National Institutes of Health NIH under award number GM070743 01 Corporate funding is provided through a contract from Unilever PLC introduction Cytoscape is a project dedicated to building open source network visualization and analysis software A software Core provides basic functionality to layout and query the network and to visually integrate the network with state data The Core is extensible through a plug in architecture allowing rapid development of additional computational analyses and features Cytoscape s roots are in Systems Biology where it is used for integrating biomolecular interaction networks with high throughput expression data and other molecular state information Although applicable to any system of molecular components and interactions Cytoscape is most powerful when used in conjunction with large databases of protein protein protein DNA and genetic interactions that are increasingly available for humans and model organisms Cytoscape allows the visual integration of the network with expression profiles phenotypes and other molecular state information and links the network to databases of functional annotations The central organizing metaphor of Cytoscape is a network graph with genes proteins and mo lecules represented as nodes and interacti
121. on ratio and green represents a high expression ratio using thresholds set for the gallRGexp experiment bundled with Cytoscape in the sampleData galExpData pvals file See the sample screenshot below 55 Cytoscape User Manual e ib Per ee piae E f i ee l i or Cpe ge e i ge ee fp a E TE BEI ypa bhp N E i a a e ea be lil id Parietal F ee eee T irr Ee EI b k ii wir r F 1 a p ne arn az kai F re Bint i i irst E a poe EHI r I 2 ce p Ga sale os i p b zi re TE TETS Ern aa N ep beer bee e T os ree Pee Visual Attributes Graph Attributes and Visual Mappers The Cytoscape VizMapper uses three core concepts e A visual attribute is any visual setting that can be applied to your network For example you can change all nodes from circles to squares by changing the node shape visual attribute e A network attribute is any data attribute associated with a node or an edge For example each edge in a network may be associated with a label such as pd protein DNA interactions or pp protein protein interactions e A visual mapper maps network attributes to visual attributes For example a visual mapper can map all protein DNA interactions to the color blue and all protein protein interactions to the color red Cytoscape allows a wide variety of visual attributes to be controlled These are summarized in the tables below 56 Cytoscape User Manual Table 17 a T
122. ons Aud y aac eal w Show Text Fil mporn Options Text File Import Ojtions Delimiter Preview Oprions CI Tab Comma semicolon Space Other Show all entries in the file W Show first LOO entrees Attribute Names Network Import Options Transfer first line as attribute names Start Import Row 1 Comment Line Default Interaction gp Reiland You can select several options by checking the Show Text File Import Options checkbox e Delimiter You can select multiple delimiters for text tables By default Tab and Space are selected as delimiters e Preview Options When you select a network table file the first 100 entries will be displayed in the Preview panel To display more entries change the value for this option If you want to show all entries in the file select Show all entries in the file You will need to click the Reload button to update the Preview panel e Attribute Names e Transfer first line as attribute names Selecting this option will cause all edge attribute columns to be named according to the first data entry in that column e Start Import Row Set which row of the table to begin importing data from For example if you want to skip the first 3 rows in the file set 4 for this option e Comment Line Rows starting with this character will not be imported This option can be used to skip comment lines in text files e Network Import Options If the Interaction Type is set to Default Interact
123. ons represented as links i e edges between nodes Development Cytoscape is a collaborative project between the Institute for Systems Biology Leroy Hood lab the University of California San Diego Trey Ideker lab Memorial Sloan Kettering Cancer Center Chris Sander lab the Institut Pasteur Benno Schwikowski lab Agilent Technologies Annette Adler lab and the University of California San Francisco Bruce Conklin lab Visit http www cytoscape org for more information License Cytoscape is protected under the GNU LGPL Lesser General Public License The License is included as an appendix to this manual but can also be found online http www gnu org copyleft lesser txt Cyto Cytoscape User Manual scape also includes a number of other open source libraries which are detailed in theCytoscape User Manual Acknowledgements below What s New in 2 5 Cytoscape version 2 5 contains several new features plus improvements to the performance and usability of the software These include e New VizMapper user interface UI e More Intuitive UI e Continuous mapping editors e Visual editor for default view e Visual Mapping Mapping Browser e Improved visual legend generator e Utilities to generate discrete values e New Features for Visual Style e Transparency opacity support e Continuous edge width e Color visual property is separated from Arrow and Edge e New Filter UI e Use intuitive UI widgets for basic filter
124. osph YBL1IO3C mitochondrial signaling Pathway tra phoesphoaprotein RTG3 5000000199 phosp YEKROS7W gluconeogenesis phosphoenolpyruvate carbo JPM2 PCK1 PPC1 S000001 FYILOOJC call wall organization and biagenasi phosphatidinosital 4 5 b6is 3 bisphasphale 5 phosphat Node Attribute Browser Edge Attribute Browser Network Attribute Browser When Cytoscape is started the Attribute Browser appears in the bottom CytoPanel This browser can be hidden and restored using the F5 key or the View gt Show Hide attribute browser menu option Like other CytoPanels the browser can be undocked by pressing the little icon in the browser s top right corner To swap between displaying node edge and network attributes use the tabs on the bottom of the panel labelled Node Attribute Browser Edge Attribute Browser and Network Attribute Browser The at tribute browser displays attributes belonging to selected nodes and or edges and the currently selected network To populate the browser with rows as pictured above simply select nodes and or edges in a loaded network By default only the ID of nodes and edges is shown To display more than just the ID click t he Select Attributes EJ button and choose the attributes that are to be displayed select various attributes by clicking on them and then click elsewhere on the screen to close the attribute list Each attribute chosen will result in one col
125. oth OBO formats version 1 0 and 1 2 Note Switching Primary Key for Go Annotation Import If node IDs in a network file are NOT DB_Object_Symbol 3rd column in Gene Association file you need to select a primary key column Click Show Mapping Options to change the key Usually DB_Object_ID can be an alternative primary key Custom Annotation Files for Ontologies Other than GO for Advanced Users e The Import Ontology and Annotation function is designed to import general ontology and annotation files Internally mapping ontology terms onto existing networks is the same as joining three data tables in Cytoscape An Ontology DAG an annotation file and network data are used in this process see the example below 101 Cytoscape User Manual Network Data ij 7P LIUSYy po TY BLUSS yey a YPLOFSWY pd YBLIOT WA 1 LROWWY pd BLIGgWy I DR146C pd BLIGgWy YIROG YY YBLIGgyy i PLA48C pd BLIGgWy 1 LROWYY pd YBLIGgWy i GLOI3C pd YBLICgWy a MRISB2C pd YBLIOSWy IROIGWY pd BLIGgWy i PL248C pd YBL111C 4 LROISW pd YBL111C Ontology Data ojname ascus lipid droplet binamespace cellular component fils a 00005611 lipid particle gif Term Olid GO 0005634 1 d namespace cellular component a det A membrane bounded organelle of eukaryotic cells in which chr 4 subset goslim generic o subset qaslim qoa Bb subset goslim_ plant i subset gaslim yeast olis a GOUU43231 intracellular
126. ou do not need to touch the field labeled Assign values to nodes using A few lines of this file are shown below GENE COMMON gallRG gal4RG gal80R gallRG gal4RG gal80R YHROSIW COX6 0 034 0 111 0 304 3 75720e 01 1 56240e 02 7 91340e 06 YHR124W NDT80 0 090 0 007 0 348 2 71460e 01 9 64330e 01 3 44760e 01 YKL181W PRS1 0 167 0 233 0 112 6 27120e 03 7 89400e 04 1 44060e 01 Option B Step 1 After loading the network load the node attribute file sampleData gal probeset na using File gt Import Node attributes This file is shown in part below Probeset YHROSIW probeset2 YHR124W probeset3 YKL181W probeset4 Step 2 After loading the node attribute file select the expression data file sampleData galExpPvals probe set pvals shown in part below GENE COMMON gal1RG gal4RG gal80R gallRG gal4RG gal80R probeset2 COX6 0 034 0 111 0 304 3 75720e 01 1 56240e 02 7 91340e 06 probeset3 NDT80 0 090 0 007 0 348 2 71460e 01 9 64330e 01 3 44760e 01 probeset4 PRS1 0 167 0 233 0 112 6 27120e 03 7 89400e 04 1 44060e 01 34 Cytoscape User Manual After selecting this file in the field labeled Assign values to nodes using select Probeset You will see that this loads exactly the same expression data as in Case 1 but provides extra flexibility in case the node name cannot be used as an identifier Detailed file format Advanced users In all expression data files any whitespace spaces and or tabs is considered
127. ource Type Local meaning that network files from the local computer will be available for importing Choose the correct file by clicking on the Select button only file types that Cytoscape recognizes will be shown and then load the network by clicking on the Import button Some sample network files of different types have been included in the sampleData folder in Cytoscape Network files in SIF GML and XGMML formats may also be loaded directly from the command line using the N option ee Import Network Import Network File Data Source Type Local _ Remote URL Please select a network file Select Import Cancel 3 18 Cytoscape User Manual Load Networks from a Remote Computer URL import The Import Networks dialog is also capable of importing network files using a URL To do this set the Data Source Type to Remote and insert the appropriate URL either manually or using URL bookmarks Bookmarked URLs can be accessed by clicking on the arrow to the right of the text field see the Bookmark Manager in Preferences for more details on bookmarks Also you can drag and drop links from web browser to the URL text box Once a URL has been specified click on the Import button to load the network 90 59A Import Network Import Network File rData Source Type Local Remote URL Import Cancel ou can specify URL by the following Type URL S
128. ow pd JK Repeat step 7 for pp protein protein interactions but select red as the edge color Then repeat steps 4 through 7 for the Edge Line Style attribute You can select the correct line style dashed or solid from the dropdown list 64 Cytoscape User Manual Edge Color interaction Mapping Type Discrete Mapping pd Po pp Loo Edge Line Style interaction Mapping Type Discrete Mapping pd a LONG_DASH pp a 2OLID Now your network should show pd interactions as dashed blue lines and pp interactions as solid red lines A sample screenshot is provided below epe Cytoscape Desktop Session galFiltered cysi Saanaa 8 BB sean Comtral Panal epea galFilte i al Curreeat Visual Style l W K R EN NA 1 Visual Mapping browser ESEA a T Edge Color interaction Mapoing Type Discrete Mapping pel 7 pp E F Edge Line Style interaction Mapping Type Discrepe Mapping pd LONG_DASH pa _ SOLID F Unused Properties Edge Font Face Edge Font Size Edge Label he a 7 Ae 4 aa TESB kA A WLO Welcome to Cytoscape 2 5 Right click drag to ZOOM Middla click drag to PAN 65 Cytoscape User Manual Tutorial 3 Visualizing Expression Data on a Network The following tutorial demonstrates how to create a new visual style using a continuous mapper The goal is to superimpose gene expression data onto a network and display gene expression values along a color
129. own user interface for editing e The lower left panel All available filters are shown in this list Initially this list will contain only sample filters but as you create more they will be added here 83 Cytoscape User Manual e The upper left panel Pressing the Create new filter button adds a filter to the Available Filters box and the Remove selected filter button deletes the currently selected filter Creating Filters Clicking the Create new filter button allows you to select a type of filter to create as shown below Filter Creation Malog Filter types Filter Type Description Meise Select nodes or edges based on the String Filter value of a numeric attribute Topology Filter Boolean Meta Filter Node Interactions Edge Interactions The important thing to realize when creating a filter is that the filter does not do anything by itself Once created the filter must be applied to the network String Filter Use Filters Manage Filters String Pattern Filter Create new Filter Remove selected Filter Available Filters Filter Name Node canonicalName Select All Filter Node canonicalName YL Select graph objects of type Node Node canonicalName YOY Node canonicalName with a value For text attribute canonicalName that matches the pattern Apply selected Filter The String Filter allows you to filter nodes or edges by a given text attribute of your current loaded network
130. p type gt nodeE nodeF nodeB nodeG nodeY lt relationship type gt nodeZ A more specific example is nodel typeA node2 node2 typeB node3 node4 noded node The first line identifies two nodes called nodel and node2 and a single relationship between nodel and node2 of type typeA The second line specifies three new nodes node3 node4 and node5 here node2 refers to the same node as in the first line The second line also specifies three relationships all of type typeB and with node2 as the source with node3 node4 and node5 as the targets This second form is simply shorthand for specifying multiple relationships of the same type with the same source node The third line indicates how to specify a node that has no relationships with other nodes This form is not needed for nodes that do have relationships since the specification of the relationship implicitly identifies the nodes as well Duplicate entries are ignored Multiple edges between the same nodes must have different edge types For example the following specifies two edges between the same pair of nodes one of type xx and one of type yy nodel xx node2 nodel xx node2 nodel yy node2 Edges connecting a node to itself self edges are also allowed nodel xx nodel Every node and edge in Cytoscape has an identifying name most commonly used with the node and edge data attribute structures Node names must be unique as identically named nodes will be treated as
131. per right corner of the CytoPanel If you select this control e g on the attribute browser panel you will now have two Cytoscape windows the main window and a new window labeled CytoPanel 2 similar to the one shown below e Bee Data Parcel ai BOs Hem i ORCANKA SECES TLF DA HANA SEQUENCE DATA E Dicer Der 1 homeleg Drosophila Mamei HPALD umara earergece oni Maipsgeh magiglnips sipngaltel gegeedihda privet Bead AMPK beia 2 Nueva HPALD umara enregat gnin mamada gerhgalcar vqugghasg kehkiengarddsmtilad siggi T54 protein HETO Sl ot HPALD unigrea eniezi Tudskegig laawagts giroa rudsgdgag pipetak vegt Peptidase Mamaia HPA unign eniresgere TTi Pruaatgenhw igne ting alfalnngrl cerrkinpay qagsivigg geeigeyctd 1 RABE Ma musculus HPA union enirezgene men migaiphice hy kagi gic Mowe harisi bdl led eetwer lic Oyskerin Himi ot nd HPAD unori enirexgene omen midierip ktkkkkerk singedvne gharefikp giingkidis jwp ieri C200RF7 7 protein Home a pita HPA umora entr exgene eis fetale iebpelineg gigise Ahrkhigol riveri aks yi iG protein coupled receptor 38 Marin is HPA uniano entre ngere amin gird ptgarenoen alpoideerd ipfaigake vibaki vorig Sigler Homo Hiplini HPAD uniata partigi m mip wojo i a iie E Tetratricopeptiide repeat domain p Mirsule HPR uniarst enirergete ami dere el pary re gGkadkigm ekipa wikaralte aea Peraxigornal bifunctional EMEY E Myre ha HFAD umara part aris mi
132. ple java lang String for Strings java lang Double for floating point values java lang Integer for integer values etc If the value is actually a list of values the class should be the type of the objects in the list If no class 1s specified in the header line Cytoscape will attempt to guess the type from the first value If the first value contains numbers in a floating point format Cytoscape will assume java lang Double if the first value contains only numbers with no decimal point Cytoscape will assume java lang Integer otherwise Cytoscape will assume java lang String Note that the first value can lead Cytoscape astray for example floatingPointAttribute firstName 1 secondName 2 5 In this case the first value will make Cytoscape think the values should be integers when in fact they should be floating point numbers It s safest to explicitly specify the value type to prevent confusion A better format would be floatingPointAttribute class Double firstName 1 secondName 2 5 Or floatingPointAttribute firstName 1 0 secondName 2 5 Every line past the first line identifies the name of an object a node in a node attribute file or an edge in a edge attribute file along with the String representation of the attribute value The delimiter is always an equals sign whitespace spaces and or tabs before and after the equals sign is ignored This means that your names and values can contain whitespace but object names c
133. pni E i E a T Ea E 36 Basic Network Navi CaliOm xcincvssaccconehscimoauidtuneswhicunewscasaeenrseenanenboanedeiiaweeruseeesetuaseinaneias 36 Other Mouse CHA VIO a isesacanantantececatsacceed anesucdstoncanneteriessoat nc ated anc Soatuaneentade ne TERET 36 Automatic Layout ALGOTS sssrin E EE 37 Layout Parmele ciernie E niei 39 Manual Lay OUl sieer Er E EE EE ETE EE 39 Node Movement and Placement 6 lt 62ic0inconcadencscatensneateedonndatiaswcaniadenadsieesrentuddencesanedveenaddens 44 pae n e E E EE E E A E AE A 44 Cytoscape User Manual NV TAS a VIS UA SOIG cance ancnsseanccenasaae sanava rear nusawsenseashonnneaanecanensrontnnsesanceeeaucaneanacantacnes 44 Introduction to the VizMapper User Interface iii cccaciccansencecancatecaesteveucsowadiwaessrieecaasetntaseed 52 Introd c c on to Visual SIylES an ccanscnasicon assed cana eicanonnsesan Gaon EEEE E E E EEE EE 53 Visual Attributes Graph Attributes and Visual Mappers cccccceceececeeeeseneeeeeeeneeaeneeas 56 Visual Siyles TMO alS 4 csndsascoracnetacsnsanhebencnasaaadesesabaae antes ae caenesenesaneaaawseseban sen caer canteen ied 60 PRON AMCEE TOMICS a E E E E E ET 70 Manacme yistal SIVIES csee e rE O 74 By Paste Visual Styles cas cctacc ta tase astintetes ENEE SEA EE EEEE ERNEA 75 Finding and Filtering Nodes and Edges nnnnsennnsssnsssssnssssresssrresssresssressssressereesssressereesseres 76 OE A T E A E A E E T E IA NE A E E TEAS 76 Erie e A A E IE EEO A O E A A T
134. point nodes have multiple names including HGNC UniProt and EntrezGene ID You can import other attribute files using these keys These imported names IDs are useful when you import GO Annota tion 99 Cytoscape User Manual Import Ontology and Annotation Tier Cine e Ta bor Import Ontology and Annotation Tuna fierce Ani ibe Amot afi oan Gena Astoiisiion Dje fae haces Cene el ae Ontology lad Cena Ontology fam Au y are el naa dented Mappieg pric Show Teer Fie ipo Opons Fitria BI Gene Association Len Click Edit Column Right Click ON OFF Colume Legent EET CEET Ey Artibai DE DR Obije iD W DE_Objet_Symbol 2 Qualifier GO ID e DEReference blae 500 GMO aS 155_ FAHA LOPUb0S 763 SGD REF SOOO 36 42 PMID 10 i hel SGD SOMO 2 HF 156 RRNA cO0003735 SGD _REF SO0O07 2642 PMatk 2g19 9 YPRIO2C TAn SOOOOO728F 155_ RRMA GO004122755 SGO REFSO00051605 PMIL2 LET d YPR 110e SGD ELTELT L55 RRA CO0043037 SCD_REFS000073642 PMIke 801_ very aw oD SOG 07 2 ER 715_ RAMA CHGS Ths COREFF 50000733 Fa PMID 67 S FR PRI1OW 500 POG T 2 es 215 RAHA GOJ003735 SOD REP S0007 3372 FiDi l l TAE 00000 728 715 RRNA Loe 2S SGD RERSOO007 5972 PMICG 7558 Y PRIZSW SCD 715 RRMA COOO2255 SGD_REF SO0OO7 3372 PMI6TS58_ PRI45W Par a J momma nam s ni 2 Err mn N e ee er 4 PRLATC game anren egg Heber of maiched Primary Key nad Lay iiriine puir Fimi 100 smiren are kaded Ter
135. preira Fie Sipe niren Aee Cee baree Cytoscape 2 4 provides a graphical user interface to import both ontology and annotation files at the same time Import Gene Ontology and Gene Association Files For convenience Cytoscape has a list of URLs for commonly used ontology data and a complete set of Gene Association files To import Gene Ontology and Gene Association files for the loaded networks please follow these steps Important All data sources in the preset list are remote URLs meaning a network connection is required Step 1 Select an Annotation File Annotation Q Gene Association file for Saccharomyces cerevisiae Please select an annotation data source Gene Association file for Saccharomyces cerevisiae iy Gene Association tile for Drosophila melanogaster vanced ig Gene Association file for Mus musculus Show Mapping g Gene Association file for Arabidopsis thaliana a Gene Association file for Caenorhabditis elegans ig Gene Association file for Rattus norvegicus Gene Assd Gene Association file for Oryza sativa Ontology vie Select File Import Ontology and Annotation to open the Import Ontology and Annotation window From the Annotation dropdown list select a gene association file for your network For example if you want to annotate the yeast network select Gene Association file for Saccharomyces cerevisiae 100 Cytoscape User Manual Step 2 Select an Ontolog
136. r result partof partof print gt gt sys stderr meaningless term np np s np np result else print result Ee Re A A E a a a a a ee a tl en e te a if len sys argv 2 print usage np np s lt someFile xml gt np np sys argv 0 sys exit inputFilename sys argv 1 print gt gt sys stderr reading np np s np np inputFilename text open inputFilename read print gt gt sys stderr read np np d characters np np len text regex lt go term gt lt go term gt cregex pre compile regex re DOTALL matches newlines m pre findall cregex text print gt gt sys stderr number of go terms np np d np np len m regex2 lt go accession gt G0 lt go accession gt lt go name gt lt go name gt cregex2 re compile regex2 re DOTALL regex3 lt go isa s rdf resource http www geneontology org go GO s gt cregex3 re compile regex3 re DOTALL regex4 lt go part of s rdf resource http www geneontology org go G0 s gt cregex4 re compile regex4 re DOTALL goodElements 0 badElements 0 print curator GO type all for term in m m2 re search cregex2 term if m2 goodElements 1 id m2 group 1 name m2 group 2 isalDs m3 re findall cregex3 term for ref in m3 isalDs append ref 110 Cytoscape User Manual m4 re findall crege
137. rary uncombined with any other library facilities This must be distributed under the terms of the Sections above b Give prominent notice with the combined library of the fact that part of it is a work based on the Library and explaining where to find the accompanying uncombined form of the same work 8 You may not copy modify sublicense link with or distribute the Library except as expressly provided under this License Any attempt otherwise to copy modify sublicense link with or distribute the Library is void and will automatically terminate your rights under this License However parties who have received copies or rights from you under this License will not have their licenses terminated so long as such parties remain in full compliance 9 You are not required to accept this License since you have not signed it However nothing else grants you permission to modify or distribute the Library or its derivative works These actions are prohibited by law if you do not accept this License Therefore by modifying or distributing the Library or any work based on the Library you indicate your acceptance of this License to do so and all its terms and conditions for copying distributing or modifying the Library or works based on it 10 Each time you redistribute the Library or any work based on the Library the recipient automatically receives a license from the original licensor to copy distribute link with or modify the Library
138. rks MCODE b i Table 6 Note A list of available Cytoscape plugins with descriptions is available online at http cytoscape org plu gins2 php The Help menu allows you to launch the online help viewer and browse the table of contents for this manual The About option displays information about the running version of Cytoscape a Help Contents F1 Contact Help Desk About Network Management Cytoscape 2 3 and newer versions allow multiple networks to be loaded at a time either with or without a view A network stores all the nodes and edges that are loaded by the user and a view displays them You can have many views of the same network Networks and their optionally associated views can be organized hierarchically An example where a number of networks have been loaded and arranged hierarchically is shown below 12 Cytoscape User Manual 508 Cytoscape Desktop New Session oi 7 fF L earch hk Control Pane SS OOC SNGryeast sif ip Network VizMapper Editor P het Nodes Edges 2354000 6156201 Sri 34110 600 270 900 3910 600 2510 2700 10110 Welcome to Cytoscape 2 5 Right click drag to ZOOM Middle click drag to FAN The network manager top right tree view in CytoPanel 1 shows the networks that are loaded Clicking on a network here will make that view active in the main window if the view exists green highlighted networks only Each network has a name a
139. rolling LOD NOTE The greater these thresholds become the slower performance will become If you work with small networks a few hundred nodes this shouldn t be a problem but for large networks it will produce noticeable slowing The various thresholds are described below Table 26 render coarseDeta1l If the sum of rendered nodes and rendered edges equals to or exceeds this number Threshold a very coarse level of detail will be chosen and all other detail parameters will be ignored If the total number of nodes and edges is below this threshold anti alias will be turned on this value defaults to 2000 render nodeBorder If the number of rendered nodes equals to or exceeds this number node borders Threshold will not be rendered this value defaults to 200 render nodeLa jlIf the number of rendered nodes equals to or exceeds this number node labels belThreshold will not be rendered this value defaults to 100 render edgeArrow If the number of rendered edges equals to or exceeds this number edge arrows Threshold will not be rendered this value defaults to 300 render edgeLa jlIf the number of rendered edges equals to or exceeds this number edge labels belThreshold will not be rendered this value defaults to 150 When printing networks or exporting to formats such as PostScript the highest level of detail is always chosen regardless of what is currently being displayed on the screen 93 Cytoscape User Manual Annot
140. rst line contains three parenthesized assignments for species type and curator In the example just above the annotation file created for budding yeast from the flat text file maintained by SGD for the Gene Ontology project and available both at their web site and at GO s shows three yeast ORFs annotated for biological process with respect to GO as described above e Following the mandatory title line there are one or more annotation lines each with the form 107 Cytoscape User Manual e canonicalName ontologyTermID e Once loaded this annotation along with the accompanying ontology can be assigned to nodes in a Cytoscape network For this to work the species type of the node must exactly match the species named on the first line of the annotation file The canonicalName of your node must exactly match the canonicalName present in the annotation file If you don t see the expected results when using this feature of Cytoscape check this again as getting either of these wrong is a common mistake Load Data into Cytoscape The easiest way to make annotations available to Cytoscape is by loading annotations into the Cytoscape annotation server This is the default behavior for the official release of Cytoscape The Annotation Manifest You must first create a text file to specify the files you want Cytoscape to load Here is an example from a file which for convenience we usually call manifest ontology goOntology txt anno
141. rview in CytoPanel 1 and the VizMapper BYGE Select Layout P Hide Control Panel Hide Data Panel Show Results Panel Open VizMapper Select The Select menu contains different options for selecting nodes and edges It also contains the Select gt Use Filters option which allows filters to be created for automatic selection of portions of a network whose node or edge attributes meet a filtering criterion Bea Plugins Help Mouse Drag Selects an Nodes p Edges p Select all nodes and edges AXA Deselect All Nodes and Edges tA Use Old Filters Use Filters 4 Layout The Layout menu has an array of features for visually organizing the network The features in the top portion of the network Rotate Scale Align and Distribute are tools for manipulating the network visual ization The bottom section of the menu lists a variety of layout algorithms which automatically lay a network out 1 Cytoscape User Manual Layout Plugins Help Rotate Scale Align and Distribute Settings J yFiles b JGraph Layouts p Cytoscape Layouts Plugins Help The Plugins menu contains options for managing install update delete your plugins and may have options added by plugins that have been installed such as the Agilent Literature Search or Merge Networks De pending on which plugins are loaded the plugins that you see may be different than what appear here Manage Plugins Update Plugins Merge netwo
142. s Aitite Manes etwork impon Opliens Trarsfer first line es tinbene names Start impor Rica Relogd Periw Bi Text File Left Click Edit Column Right Click ON OFF Column Legend Alias pakupis py as Eey Atirihwies T l YPRO62W W GENE COMMON X gall gal4RG a galfOR W ali Einaste YHROSIW CONG 111 0 304 A757 200 01 al YHR124W MDT 007 0 348 271450 0 2 YPR1026 YKL181W PRS1 0 233 0 112 G 27120e 05 YPR 110C YGROF2W UPF3 0 471 0 787 410450 0 YPR113W YHLOZOC OPII 0 015 0 151 140L60e 04 pa YGRI45W YGRI45W 0577 088 5 37920 03 TPR 119W YGLO41 YOLO41 0 086 0 103 4460S0e 04 YPR124W YOR 18 CRM1 000i 0 018 6 13810e0 01 E YPRLI4ASW Lc ET ot A ia i m T T C a iien Mn E a E T she en Ps Son PR 167C aber of matched Priman Kew md Key Aiiribube pair 9 First 100 entries ae loaded for preview File Sine 815 Fayed im part d Sample Attribute Table 1 Table 12 AAC3 YBRO85WIANC3 SO00000289 AAT2 YLRO27CIASP5 S000004017 BIK1 YCLO29CIARMSIPAC 14 SO00000534 The attribute table file should contain a primary key column and at least one attribute column The maximum number of attribute columns is unlimited The Alias column is an optional feature as is using the first row of data as attribute names Alternatively you can specify each attribute name from the File Import gt Attribute from Table text MS Excel user interface Basic Operation The user interface of the Import Attributes from Tabl
143. s Waihi dhh jsm g Se BE YL hw Pay iglieo as tucaies poe ei DD reed rn ole A poe Croc mete mateo kiaii late Boome TRIDA pipik hia i e Hip Ph aml Tgi oF pa g Dj ge ee aii Mapia a eee ia e 4 Bimi kiirii Fostar che Anrini bosi peck Attire Fosa Basic Usage Cytoscape includes four CytoPanels Control Panel on the left Tool Panel on the bottom of Control Panel Data Panel on the bottom and Result Panel on the right By default Control Panel and Data Panel will appear Result Panel may appear depending on the mix of Cytoscape plugins that you currently have installed Tool Panel will appear when you select the following commands under the Layout menu Rotate Scale and Align and Distribute All panels can be shown or hidden using the View gt Show Hide functions Be Select Layout P Hide Control Panel Hide Data Panel Show Results Panel Open VizMapper In addition CytoPanels can be floated or docked by selecting the icon at the top right corner of each CytoPanel The icon and tooltip will change based on the CytoPanel state If the CytoPanel 1s docked clicking on the icon will float the CytoPanel as indicated by the Float Window tooltip Alternatively if the CytoPanel is floating clicking on the icon will dock the CytoPanel as indicated by the Dock Window tooltip jd naj Float Dock Wincow Window 92 Cytoscape User Manual Rendering Engine What is Level of Detail LOD I
144. s e Suggest search values with indexing e Have options to save in session or globally e Layout Manager Broker e Plugin Manager and new plugin website e Install Update Delete plugins from within Cytoscape e Search for version compatible plugins from any host site e Display list of installed plugins e Undo Manager e Group API for plugin developers e Node stacking e Tested on both Java SE 5 and 6 e Many many bug fixes Cytoscape User Manual Launching Cytoscape Cytoscape is a Java application verified to run on Linux Windows and Mac OS X Although not officially supported other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 5 or later is available for the platform System requirements The system requirements for Cytoscape depend on the size of the networks the user wants to load view and manipulate Table 2 TO i Small Network Visualization Large Network Analysis Visualization Processor As fast as possible Graphics Card On board Video Highend Graphics Card Monitor XGA 1024X768 Wide or Dual Monitor Getting Started Install Java Memory siavi If not already installed on your computer download and install Java SE 5 or 6 Cytoscape 2 5 will no longer run with Java version 1 4 x or lower You must install Java SE 5 or 6 These can be found at Java SE 5 Java SE 6 In general Java SE 6 is faster than 5 If your machine is compatible with the 6 series please try version 6
145. s use the same format Node attribute file names often use the suffix noa while edge attribute file names use the suffix eda Cytoscape re cognizes these suffixes when browsing for attribute files Node and edge attributes may be loaded at the command line using the n and e options or via the File Import menu 21 Cytoscape User Manual When expression data is loaded using an expression matrix it is automatically loaded as node attribute data unless explicitly specified otherwise Node and edge attributes are attached to nodes and edges and so are independent of networks Attributes for a given node or edge will be applied to all copies of that node or edge in all loaded network files re gardless of whether the attribute file or network file is imported first Note In order to import network attributes in Cytoscape 2 4 please go to File Import Attribute from Table text MS Excel or encode them in an XGMML network file see Supported File Formats for more details Detailed file format Advanced users Every attribute file has one header line that gives the name of the attribute and optionally some additional meta information about that attribute The format is as follows attributeName class formal class of value The first field is always the attribute name it cannot contain spaces If present the class field defines the formal package qualified name of the class of the attribute values For exam
146. seen at http www geneontology org GO current annotations shtml The rightmost column contains links to tab delimited files of gene associations by species Choose the species you are interested in and click Download Let s use GO Annotations EBI Human as an example After you have downloaded and saved the file look at the first few lines protein taxon 9606 protein taxon 9606 SPTR 000115 DRN2_HUMAN GO 0003677 PUBMED 9714827 TAS F Deoxyribonuclease II precursor IP100010348 SPTR 000115 DRN2_HUMAN GO 0004519 GOA spkw IEA F Deoxyribonuclease II precursor IP100010348 SPTR 000115 DRN2_HUMAN GO 0004531 PUBMED 9714827 TAS F Deoxyribonuclease II precursor IP100010348 protein taxon 9606 Note that line wrapping has occurred here so each line of the actual file is wrapped to two lines The goal is to create from these lines the following lines species Homo sapiens type Molecular Function curator G0 IP100010348 0003677 TP100010348 0004519 TP100010348 0004531 Or species Homo sapiens type Biological Process curator GO NP_001366 0006259 NP_001366 0006915 NP_005289 0007186 NP_647593 0006899 The first sample contains molecular function annotations for proteins and each protein is identified by its IPI number IPI is the International Protein Index which maintains cross references to the main databases for human mouse and rat proteomes The second sample contains biological process annotation and
147. so represents its corresponding protein Nodes may also be used to represent compounds and reactions or anything else instead of genes If anetwork of genes or proteins is to be integrated with Gene Ontology GO annotation or gene expression data the gene names must exactly match the names specified in the other data files We strongly encourage naming genes and proteins by their systematic ORF name or standard accession number common names may be displayed on the screen for ease of interpretation so long as these are available to the program in the annotation directory or in a node attribute file Cytoscape ships with all yeast ORF to common name mappings in a synonym table within the annotation directory Other organisms will be supported in the future Why do we recommend using standard gene names All of the external data formats recognized by Cyto scape provide data associated with particular names of particular objects For example a network of protein protein interactions would list the names of the proteins and the attribute and expression data would likewise be indexed by the name of the object The problem is in connecting data from different data sources that don t necessarily use the same name for the same object For example genes are commonly referred to by different names including a formal location on the chromosome identifier and one or more common names that are used by ordinary research ers when talking about that gene
148. tation yeastBiologicalProcess txt annotation yeastMolecularFunction txt annotation yeastCellularComponent txt Use the Cytoscape b command line argument to specify the annotation manifest file to read e g b manifest Please note that the s switch which sets the default species for your data is required to exactly match the species named in any annotation file you wish to use Getting and Reformatting GO Data The Gene Ontology GO project is a valuable source of annotation for the genes of many organisms In this section we will explain how to 1 Obtain the GO ontology file 2 Reformat it into the simpler flat file Cytoscape uses 3 Obtain an annotation file we illustrate with yeast and human annotation 4 Reformat the annotation files into the simple Cytoscape format Obtain the GO ontology file Go to the GO XML FTP ftp ftp geneontology org pub go xml page Download the latest go YYYYMM termdb xml gz file Reformat GO XML ontology file into a flat file gunzip go YYYYMM termdb xml gz python parseGoTermsToFlatFile py go YYYYMM termdb xml gt goOntology txt see below for Python script listing Obtain the association file for your organism GO maintains a list of association files for many organisms these files associate genes with GO terms The next step is to get the file for the organism s you are interested in and parse it into the form Cytoscape 108 Cytoscape User Manual needs A list of files may be
149. tna Girne vl dikegigkaw a eaga air OF box and WD 40 domain protein 5 Ha eia HPAD unary eRe noe gimn mdeggie dikyqifs lpsadvuug Mongeqavs rdehareg rrari Fxceniial meiotic eadonucleace Wy org Ea HPA RER Aa iaai makk gag degt afaina giir agir tekken docaroaa T J a F lt m e e e e e e a o a e e e e e a ae o a e o o a a e Mode Attribute Browser Edge Attribute Browser Webwork Attribute Browser Note that CytoPanel 2 now has a Dock Window control If you select this control the window will dock onto the main window Cytoscape also has an editor that enables you to build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window The Node shapes and Edge arrows on the palette are defined by the currently used Visual Style To edit a network just select the Ed itor tab on CytoPanel 1 An example of an editor with the palette contained in CytoPanel 1 and defined by the BioMoleculeEditor Visual Style is shown below Cytoscape User Manual e e ee Cytoscape Desktop New Session DRAAD AR o B Control Panel 4 enea Sample Network 1 e Network VizMapper Editor P Directed Edge Add a Node ad Data Pare ral Sig JSR IC CeO cee nodes rode n O Node Attribute Browser Edge Attribute Browser Network Attribute Browser Welcome to Cytoicape 2 5 Right click drag to ZOOM Middle click drag to PAN The Menus File The Fi
150. to connect the genes present in different data sources even if they have different names as long as those names are recognized by the synonym server For this to work Cytoscape must also be provided with the species to which the objects belong since the data server requires the species in order to uniquely identify the object referred to by a particular name This is usually done in Cytoscape by specifying the species name on the command line with the P option cytoscape sh P defaultSpeciesName Saccharomyces cerevisiae or by editing the properties under Edit Preferences Properties The automatic canonicalization of names can be turned off using the P option cytoscape sh P canonic alizeName false or by editing the properties under Edit Preferences Properties This canonicaliz ation of names currently does not apply to expression data Expression data should use the same names as the other data sources or use the canonical names as defined by the synonym table Node and Edge Attributes Interaction networks are useful as stand alone models However they are most powerful for answering scientific questions when integrated with additional information Cytoscape allows the user to add arbitrary node edge and network information to Cytoscape as node edge network attributes This could include for example annotation data on a gene or confidence values in a protein protein interaction These attributes can then b
151. to specify a different Node Label using the VizMapper Currently there is no mechanism to check whether the constructed URL query is correct and if the node label is meaningful Similarly there is no ID mapping between various identifiers For example a link to NCBI Entrez from a network that uses ensembl gene identifiers as node labels will produce a link to Entrez using ensembl ID which results in an incorrect link It is the user s responsibility to ensure that the node label that is used as the search term in the URL link will result in a meaningful link Adding or Removing Links The default links are defined in a linkout props file contained in linkout jar These links are normal java properties and can be edited by going to Edit Preferences Properties New links can be defined this way as well New links can be defined at startup in a separate file and loaded from the command line either by specifying a file containing the links cytoscape sh P new_linout props or as individual properties cytoscape sh P linkouturl yeast SGD http db yeastgenome org cgi bin locus pl locus 1D Any links defined on the command line will supersede the default links To remove a link from the menu simply delete the property using Edit Preferences Properties 105 Cytoscape User Manual Acknowledgements Cytoscape is built with a number of open source third party Java libraries The Cytoscape team gratefully acknowledges the following
152. tor i A i i AAA A Al Al Al ll A AMA Curren Visual Sryl joe M A M a ii ha a l Ml l aA ee oo H i i A ct dk a A AA Ok a kk Ce fasts i dk ek kd A A ek kk ee hhk ee eee ee ee er ae ae ee iida a a dk ke ek a kk Gti a th ad ak E 4 44 RA Re See Ak tei ual Pal app mig irritar k A k mia t aE a Dr ar Aa A Aji d lo ee aJa La a dadl a d ha ee eee eee A a keke ee eee ae r a a E Edge Fom Face Dheir oo cra Aug amp sd dk ek AO a kkk kd kk Edge Fore Sie Doub Cik i cre kd A kk A eee SE A Oe Kn A Ok Edge Labe Cele Chek y cre iL iii i i i iid iii EAA i Edge Label Color Goutle Click to cre ee Edge Line Soe Dowie Chick i cre Edge Lire Width Dbk Chick oo rE Edge Onprin Dawe Chick oo cra a SSS Fe Edge Sourte Arica Dove Click to cre Edge Source Arrow Gauble Clck oo cre i Pacer Warre Arrn Diae re ri pre Kiek Arm Eae Brai ir Nede Attribute Browser Edge Attribute Sowier Welcome ta Lytoprape 2 5 Right click drag to ZECH JM Miidle click ang to FAH Tutorial 2 Creating a New Visual Style with a Discrete Mapper The following tutorial demonstrates how to create a new visual style using a discrete mapper The goal is to draw protein DNA interactions as dashed blue lines and protein protein interactions as solid red lines Step 1 Load a sample network From the main menu select File Import gt Network Multiple file types and select sampleData galFi
153. umn in the attribute browser Most attribute values can be edited by double clicking an attribute cell list values cannot be edited and neither can the ID Attribute rows in the browser can be sorted alphabetically by specific attribute by clicking on a column heading A new attribute can be created using the Create New A t t r 1 b u t e O button and must be one of four types integer string real number floating point or boolean Attributes can be deleted using the Delete Attributes 4 Mi button NOTE Deleting attributes removes them from Cytoscape not just the attribute browser To remove attributes from the browser without deleting them simply unselect the attribute using the Select 32 Cytoscape User Manual A t t r 1 b u t e S EJ button The right click menu on the Attribute Browser has several functions such as exporting attribute information to spreadsheet applications For example use the right click menu to Select All and then Copy the data and then paste it into a spreadsheet application Each attribute browser panel also has a button for importing n e W a t t r 1 b u t e S The Node Attribute Browser panel has additional buttons for loading Gene Expression attribute matrices as node attributes Loading Gene Expression Attribute Matrix Data In addition to normal node and edge attribute data Cytoscape also supports importing gene expression data Gene expression data are imported using a dif
154. ute values as shown below 68 Cytoscape User Manual 8Ae Cytoscape Desktop New Session EUa pag gt i Cortrol Pare fal ADA galFiltered sif i Network VieMapper Editor b i Curent Visaal Style default H be T Defaults Visual Mapping Browser H Ea T Mode Wisual Mappia T Mode Color Degree Wapping Type Daire Mapprg l es Z Cc j E 4 5 C 5 I 7 E A a 11 CN 17 E 7 Welcome te Lytoacape 2 5 Hagnt click drag te 200M Middla clitk drag to PAN 8 Cretate a Discrete Node Size Mapping Select Degree as controlling attribute 9 Select Node Size and right click to show popup menu Select Generate Discrete Values gt Series Numbers Only Type 30 for the first value and click OK Enter 5 for increment 10 Apply Force Directed layout Final view of the window looks like the following 69 Cytoscape User Manual 8 A Cytoscape Desktop New Session enasna b iia Comino Paral af galFiltered sif Network VigMagper Editar F Current Visaal Style default al hel T Detauls Visual Mapping browser a E T Mode Visual Mapping T Node Sze Degree Happing Type Getcrete Mapping i l 0 0 45 0 J 60 0 F450 20 0 105 0 120 0 150 0 5 E 1350 g 1 165 0 Li 1LB00 Welcome toe Lytoacape 2 5 Hagnt click drag te ULIM Middla clitk drag to PAN Advanced Topics Editing Discrete Mappings From version 2 5 se
155. value of 0 034 with significance measure 3 75720e 01 Some variations on this basic format are recognized see the formal file format specification below for more information Expression data files commonly have the file extensions mrna or pvals and these file extensions are recognized by Cytoscape when browsing for data files General Procedure Load an expression attribute matrix file using File Import gt Attribute Expression Matrix to bring up the import window or by specifying the filename using the m option at the command line If you use the command line input you must enter your expression data by node ID If you use the dialog box then you can either load expression data by node ID the default option or you can select a node attribute to use in assigning your expression data to your Cytoscape nodes If you do use a node attribute then 1 the at tribute should already be loaded and 2 the node attribute value must match the first column in your matrix file Worked Example For the sample network file sampleData galFiltered sif Option A Load a sample gene expression data set by going to File Import gt Attribute Expression Matrix In the resulting window in the field labeled Please select an attribute or expression matrix file use the Select button to enter sampleData galkxpData pvals The identifiers used in this file are the same ones used in the network file sampleData galFiltered sif so y
156. veral utility functions are available for Discrete Mappings You can use those functions by right clicking anywhere on the Visual Mapping Browser shown below grin Eimi Cirno I 3 Delete mapping E Generate Discrete Values a Rainbow I Modify Discrete Values H Rainbow 2 w modulations Randomize Series Number Only Fit Node Width to Label _ 4 Edit selected values at once 4 Lock Node Width Height vu F 4 75 0 Automatic Value Generators e Generate Discrete Values Functions in this menu category are value generator for discrete mappings Users can set values for discrete mappings automatically by these functions e Rainbow 1 and Rainbow 2 These functions try to assign as different colors as possible to each values see the example below 70 Cytoscape User Manual Y Node Color Degree Mapping Type Discrete Mapping 1 3 3 4 5 6 7 8 9 11 17 18 e Randomize Randomize colors and numbers If you use this function for numerical values node size Opacity etc you need to specify a range For example if you want to set values from 1 to 100 you need to type 00 in the dialog e Series Set series of numbers to the specified mapping oe Fe ir Ht visual Mapping Browser BE m T Node Size Degree Mapping Type Discrete Mapping 20 0 35 0 0 0 65 0 80 0 95 0 110 0 125 0 140 0 155 0 kil a B e Fit node size to label This function is only for no
157. www blueprint org bind bind_downloads html From von Mering et al Nature 417 399 2002 and Lee et al Science 298 799 2002 xkk Created from Cytoscape tutorial web page Original data sets are available at http www cyto scape orghttp cytoscape org cgi bin moin cgi Data_Sets from A merged human interactome by Andrew Garrow Yeyejide Adeleye and Guy Warner Unilever Safety and Environmental Assurance Center Launch the application Double click on the icon created by the installer or by running cytoscape sh from the command line Linux or Mac OS X or double clicking cytoscape bat Windows Alternatively you can pass the jar file to Java directly using the command java Xmx512M jar cytoscape jar p plugins The Xmx512M flag tells java to allocate more memory for Cytoscape and the p plugins option tells cytoscape to load all of the plugins in the plugins directory Loading the plugins is important because many key features like layouts filters and the attribute browser are included with Cytoscape as plugins in the plugins directory See the Command Line chapter for more detail In Windows it is also possible to directly double click the jar file to launch it However this does not allow specification of command line arguments such as the location of the plugin directory Cytoscape User Manual When you succeed in launching Cytoscape a window will appear that looks like this captured on Mac OS 10 4 ane a SAAR AR
158. x4 term partofIDs for ref in m4 partofIDs append ref flatFilePrint id name isaIDs partofIDs else badElements 1 print gt gt sys stderr no match to m2 print gt gt sys stderr Viens pes Naas ee np np term Q print gt gt sys stderr goodklements np np d np np goodElements Q print gt gt sys stderr badElements np np d np np badElements Script 2 parseAssignmentsToFlatFileFromGoaProject py import sys def fixCanonicalName rawName for instance trim YBRO85W ANC3 to YBRO85W bar rawName find if bar lt 0 return rawName return rawName bar def fixGoID rawID bar rawlD find 1 return rawID bar def readGoaXrefFile filename lines open filename read split n result for line in lines if len line lt 10 continue tokens line split t ipi tokens 2 np tokens 5 semicolon np find if semicolon gt 0 np np semicolon if len ipi gt 0 and len np gt 0 result ipi np return result if len sys argv 3 print error parse lt gene_associations file from GO gt lt goa xrefs file gt sys exit associationFilename sys argv 1 xrefsFilename sys argv 2 species Homo sapiens ipiToNPHash readGoaXrefFile xrefsFilename tester IPI00099416 print hash size np np d np np len ipiToNPHash print test map np np s
159. y File Ontology Gene Ontology Full vanced m Generic GO slim Yeast GO slim Molecule role NOH Protein name family name ontology EVEN Event NOH pathway ontology ft Click Edit Protein protein interaction Show Mapping Select an Ontology data OBO file from the Ontology dropdown list If the file 1s not loaded yet it will be shown in red The first three files are Gene Ontology files You can load other ontologies but you need your own annotation file to annotate networks Step 3 Import the files e Once you click the Import button Cytoscape will start loading OBO and Gene Association files from Step 4 the remote sources If you choose GO Full it may take a while since it is a large data file e When Cytoscape finishes importing files the import window will be automatically closed All attributes mapped by this function have the prefix annotation and look like this annotation attribute_name All ontologies will be added to the end of the Ontology DAGs branch in the Network Manager aca aca 219740 34892 129 373 149 5 3737 530 i 84800 B86 2 Ontology DAGs have some attributes associated with the terms All attributes associated with ontology terms will have the prefix ontology They have at least one attribute ontology name For more detailed in formation about attributes for ontology DAGs please read the official OBO specification document e Note Cytoscape supports b
160. y file and human Gene Association files because the Gene Association file is only compatible with GO Visualize and Browse Ontology DAG for Advanced Users Relationships between ontology terms are usually represented as Directed Acyclic Graphs DAGs This is a special case of a network or graph where nodes are ontology terms and edges are relationships between terms Originally Cytoscape used a special data structure called BioDataServer to store ontology DAGs Starting in version 2 4 ontology data will now be stored in the same data structure as normal net works This enables users and plugin writers to visualize browse and manipulate ontology DAGs just like other networks The following is an example of visualization of an ontology DAG Generic GO Slim 96 Cytoscape User Manual Every ontology term and relationship can have attributes In the OBO files ontology terms have optional fields such as definition synonyms comments or cross references These fields will be imported as node attributes To browse those attributes please use the attribute browser see the example below SL LE wiog Fare meno oper def LOAOGROI IE nuclear chroeicsome amp Chrerme Tour in ihe pucks of a eukaryotic cel GEDHI oaoplatine camioane Chrome Toud Re oO ole GOhKOG0SS7 S colular comporti Th pat of a cdl o its eatracelular eraronment in whith 2 gene produc it located A gane pradu may ba located in one or LODRISS 76 xiracelular regio
161. y it with the complete corresponding machine readable source code which must be distributed under the terms of Sections and 2 above on a medium customarily used for software interchange If distribution of object code is made by offering access to copy from a designated place then offering equivalent access to copy the source code from the same place satisfies the requirement to distribute the source code even though third parties are not compelled to copy the source along with the object code 114 Cytoscape User Manual 5 A program that contains no derivative of any portion of the Library but is designed to work with the Library by being compiled or linked with it is called a work that uses the Library Such a work in isol ation is not a derivative work of the Library and therefore falls outside the scope of this License However linking a work that uses the Library with the Library creates an executable that is a derivative of the Library because it contains portions of the Library rather than a work that uses the library The executable is therefore covered by this License Section 6 states terms for distribution of such executables When a work that uses the Library uses material from a header file that is part of the Library the object code for the work may be a derivative work of the Library even though the source code is not Whether this is true is especially significant if the work can be linked without the Library

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