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Cytoscape 2.1

1. s s s s id name isa partof result result strip if result isa isa or result partof partof print gt gt sys stderr meaningless term s result else print result if len sys argv 2 print usage s lt someFile xml gt sys argv 0 sys exit inputFilename sys argv 1 print gt gt sys stderr reading s inputFilename text open inputFilename read print gt gt sys stderr read sd characters 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 d len m regex2 lt go accession gt GO 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 GO s gt cregex4 re compile regex4 re DOTALL goodElements 0 badElements 0 print curator GO type all for term inm m2 re search cregex2 term if m2 goodElements 1 id m2 group 1 name m2 group 2 isaIDs m3 re findall cregex3 term for ref in m3 isaIDs append ref m4 re findall cregex4 term partofIDs for ref in m4 partofIDs append ref
2. and parse it into the form Cytoscape needs A list of files may be 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 SPTR 000115 DRN2_HUMAN GO 0003677 PUBMED 9714827 TAS F Deoxyribonuclease II precursor IPI00010348 protein taxon 9606 SPTR SPTR 000115 DRN2_HUMAN GO 0004519 GOA spkw IEA F Deoxyribonuclease II precursor IPI00010348 protein taxon 9606 20020425 SPTR SPTR 000115 DRN2_HUMAN GO 0004531 PUBMED 9714827 TAS F Deoxyribonuclease II precursor IPI00010348 protein taxon 9606 SPTR 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 GO IPI00010348 0003677 IPI00010348 0004519 IPI00010348 0004531 or species Homo sapiens type Biological Process curator G0 NP_001366 0006259 NP_001366 0006915 NP_005289 0007186 NP_647593 0006899 The first sample contains molecular function annotation 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 mo
3. isa 90001 Lipid Metabolism isa 90001 Energy Metabolism isa 90001 Nucleotide Metabolism isa 90001 Amino Acid Metabolism isa 90001 Metabolism of Other Amino Acids isa 90001 Metabolism of Complex Carbohydrates isa 90001 The format has three required features I 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 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 Following the mandatory title line there are one or more category lines each with the form number0 name isa partof numberl number2 isa and partof are terms used in GO they describe the relation between parent and child terms in the ontology hierarchy 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 G0 YMRO56C 0006854 YBRO85W 0006854 YJR155W 0006081 and from KEGG species Mycobacterium tuberculosis type Metabolic Pathways curator KEGG RVO761C 10 RVO761C
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6. 71 RVO761C 120 RVO761C 350 RVO761C 561 RV1862 10 The format has these required features 1 The first line contains three parenthesized assignments for species type and curator In the example just above the annotation file which we create 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 described further above 2 Following the mandatory title line there are one or more annoation lines each with the form canonicalName ontologyTermID 3 Once loaded this annotation along with accompanying ontology can be assigned to nodes in a Cytoscape network For this to work the species type of the node must agree exactly with 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 In Process The easiest way to make annotation available to Cytoscape is by loading annotation into an in process annotation server This is the default 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
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8. YOU Diss siccccsdecsecteccetscososesecesscsvecesbavaacoeccssnuesacscocessseuecbebavsocsonsooscdaesecocessvoeeeosevvecvaseuaccass 22 ISA IN vasvostedednccecsedosebedadvoceaceshedvededelosedeesvcsesbednnseesessesesdeSeasedsedbedescedesesvsvevesvecseaee 24 9 1 INTRODUCTION TO VISUAL STYLES 0 ia A es 24 9 2 VISUAL ATTRIBUTES GRAPH ATTRIBUTES AND VISUAL MAPPERS co cccccooooonoconononoconnncnnnnnnnccnnnnnnnonnnnncnnnnnnncnnnnnos 27 9 3 TUTORIAL CREATING A NEW VISUAL STYLE ccssssccccccecesssnececececsesseceecececeesessaaeceecesesesaaeceeeesesensaaeeeeeeeees 30 9 4 TUTORIAL CREATING A NEW VISUAL STYLE WITH A DISCRETE MAPPER scsescsscceceesessceceeeceesensaeceeeeeeees 32 9 5 TUTORIAL VISUALIZING EXPRESSION DATA ON A NETWORK ccccessssssseeeeeceesesececececseseueausceceeeesensaseeeeeeees 33 LOS DET AA soosonseetossussockorescecs cnsebentsesoes vacdeabechose daskdosene cassdeusabcuees sscsseceuaee 34 TT ACKNOWLEDGEMENTS vecsietessusceseseceveibced cadet cote tascndecseseusuetecced suse seus esoo sdevensa Sosssdovteconetebesseiectadessoetosteccnse 39 APPENDIX ANNOTATION SERVER FORMAT cccccccssssssscsssssscsseccccccsssscsseccccssssssssenccescssssesenecessessssssenseees 40 INTRODUCTION coda tandil ted 40 BUILDING YOUR OWN ANNOTATION FILES ccccessesssceccceceessnececececsensnsnsaeceeececsessauececeescsessaeceeececsesenseaeeeeseseseneaeees 40 LOAD DATA IN BROCES SS uta rada 42 GETTING AND REFORMATTING GO DATA wu cc cccccess
9. every attribute value should be specified as a list and every member of the list should be of the same class Again the class will be inferred if it is not specified in the header line Lists are not supported by the visual mapper so can t be mapped to visual attributes 8 Navigation and Layout BASIC FEATURES Use the zooming buttons located on the toolbar to zoom in out of the interaction network shown in the current network display Zoom icons are detailed below Ste 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 Use the left mouse button to select a node hold down the Shift key to select more than one node Use the right mouse button to launch a context sensitive menu with additional information about the node that was clicked on NETWORK LAYOUT To lay out your network using a Spring Embedded Layout select Layout gt Apply Spring Embedded Layout from the main menu Sample screenshot is provided below Cytoscape File Edit Data Select Layout Visualization Plugins Filters b Q 4 Cele e K Cytoscape Desktop gt PASHAZOXADE IA Network Node Edge 331 362 Nodes 331 0 selected Edges 362 0 selected Figure Applying the Spring Embedded Layout to a sample network 9 Visual Styles With th
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11. integer value for each experimental condition 7 Node and Edge Attributes Cytoscape allows the user to add arbitrary node and edge information to Cytoscape as node and edge attributes Attributes could be for example annotation data on a gene or confidence values in a protein protein interaction These attributes can then be visualized in a custom user defined way by setting up a mapping from data attributes to visual attributes colors shapes etc see section 9 Visual Styles Node and edge attribute files are very simply formatted A node attribute file begins with the name of the attribute on the first line and on each following line has the name of the node followed by an equals sign followed by 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 YALOO1C metabolism YAROO2W apoptosis YBLOO7C 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 following is an example edge attributes file InteractionStrength YALOO1C pp YBRO43W 0 82 YMRO22W pd YDL112C 0 441 YDL112C pd YMRO22W 0 9013 Cytoscape treats edge a
12. line is a header line with one of the following three 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 are ignored these columns will contain names for each gene The next 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 fields This format specifies data with ratios but no significance values 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 LAmBpas token This format specifies both ratios and significance values Each line after the first is a data line with the following format FormalGeneName CommonGen
13. no way to smoothly morph between circular nodes and square nodes The matrix below shows visual mapper support for each visual property El 2 3 E Lg n 3 E 38 BE Sa a8 2E ss as A2 Oe Node Properties Node Color O O Node Border Color O e Node Border Type O O D Node Shape 9 0 D Node Size O O O Node Label 0 0 D Node Font Family O O D Node Font Size O O O Edge Properties Edge Color 9S 0 g Edge Line Type O O D Edge Source Arrow 0 D Edge Target Arrow O O D Edge Label 0 0 D Edge Font Family O O D Edge Font Size 9 0 o Legend Mapping is not supported for specified visual property 0 Mapping is fully supported for specified visual property Mapping is partially supported for specified visual property Support for continuous to continuous mapping is not supported 9 3 Tutorial Creating a New Visual Style To create a new visual style select Visualization gt Set Visual Properties from the main menu or select the color wheel icon in the main button bar You will now see a new Visual Styles dialog box shown at right Visual Styles default Visual Styles 3 Define New Duplicate Rename Delete Close Visual Property Categories Click the New button and enter a name for your new visual style e ale et Viswal Peopesti when prompted Then click the Define button You wi
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15. 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 cannot contain an equals sign and no guarantees are made concerning leading or trailing whitespace Usually the object names should be the same as the names in your graph file unless name conversion is being used see the section on name resolution in section 5 Building and Storing Interaction Networks Edge names are all of the form sourceName edgeType targetName Note that this format is different from the specification of interactions in the SIF file format To be explicit in a SIF file an interaction looks like sourceNam dgeType targetNam To set an attribute for the edge defined by this interaction the matching line in a attributes file should look like sourceName edgeType targetName valu Yes this is confusing we re planning on fixing this in the next file format update for Cytoscape To specify lists of values use the following syntax listAttributeName class java lang String firstObjectName firstValue secondValue thirdValue secondObjectName onlyOneValue This defines an attribute which is a list of Strings The first object has three strings and thus three elements in its list while the second object has a list with only one member In the case of a list
16. size Visual Attributes Associated with Edges Edge Color Edge Line Type The following options are available EE AAE Edge Source Arrow The following options are available elt Iv fet Na Edge Target Arrow The following options are available el Tv Na Edge Label the text label for each edge Edge Font edge font and size Global Visual Properties e Background Color For each visual attribute you can specify a default value or define a visual mapping Cytoscape currently supports three different types of visual mappers e Passthrough Mapper graph attributes are passed directly through to visual attributes A passthrough mapper only works for node edge labels For example a passthrough mapper can draw the common gene name on all nodes e Discrete Mapper discrete graph attributes are mapped to discrete visual attributes For example a discrete mapper can map all protein protein interactions to the color blue e Continuous Mapper continuous graph attributes are mapped to visual attributes Depending on the visual attribute there are two types of continuous mappers o continuous to continuous mapper for example you can map a continuous value 0 1 to a color gradient red green or node font size 10 100 o 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 However there is
17. the filter does not do anything by itself Once created the filter must be run String Filter Use Filters 000 Manage Filters z Node Interactions Boolean Filter Topology Filter Numeric Filter String Filter Add current fiter Remove selected filter String Filter Select nodes or edges based on regular expression match to text attribute Available Filters Filter Name Node canonicalName Select graph objects of type Node with a value for text attribute canonicalName al ALIASES that matches the regular expressi commonName species Available Actions C Select Passed _ Hide Failed Go Update List of Attributes The String Filter allows you to choose to Filter Node or Edges and gives you a list of available attributes to search for each those attributes that are loaded on the network If you have the filters dialog box active and you load new graph attributes you can click the update button to refresh the attribute list Search terms are entered in the text box at the bottom For example to match any Node whose canonicalName starts with YDL you would select Node canonicalName and type YDL The is important as it matches anything for 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 typ
18. vt VT secondaryView Threshold 2000 integers gt 0 Property name Default Valid values Related value command line argument viewType tabbed tabbed plugins comma separated list of jar files p containing plugins or URL s to jar files plugin containing plugins e g JLD http server my plugin jar JLW JLL Java System properties Cytoscape also honors a new Java system property introduced in Java 1 4 java awt headless This property allows the Java system to run without Graphics support Cytoscape running in this mode allows users to run non graphical analyses as batch jobs or on systems without keyboard mouse display capabilities such as compute servers Djava awt headless true false Similar to command line argument headless noView run in headless mode do not create and display the GUI 5 Building and Storing Interaction Networks Cytoscape reads an interaction network in two ways from a simple interaction file SIF or sif format or from a standard format known as Graph Markup Language GML or gml format SIF specifies nodes and interactions only while GML stores additional information about network layout and allows network data exchange with a variety of other network display programs Typically SIF is used to import interactions when building a network for the first time since it is easy to create in a text editor or spreadsheet Once the interactions have bee
19. 0 CAA70591 327 AGPS 8540 AGPS SP 000124 IPI00010353 ENSP00000265616 ENSP00000322580 NP_005662 BAA18 958 BAA18959 AAH20694 7993 D8S2298E Note that line wrapping has occurred here each line in this 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 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 python parseAssignmentsToFlatFileFromGoaProject py gene_association goa_human xrefs goa See below for Python script listing Python script examples These scripts 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 SRevision 1 3 SDate 2003 05 18 00 38 43 import re pre sys def flatFilePrint id name isalDs partofIDs isa if len isaIDs gt 0 isa isa for isaID in isalDs isa isalD isa isa partof if len partofIDs gt 0 partof partof for partofID in partofIDs partof partofID partof partof result
20. 2se 1 4 2 download html 3 Launch the application 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 jar cytoscape jar 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 annotation data directory see the section 4 Command Line Arguments for details On Mac OS X users who downloaded the Mac OS X version of Cytoscape can double click on the Cytoscape icon to start Cytoscape Either double clicking or dragging onto the Cytoscape application any sif or gml file will load that file into Cytoscape Cytoscape Window When you succeed in launching Cytoscape a window will appear that looks like this e090 Cytoscape Desktop File Edit Data Select Layout Visualization Plugins Help CAPEK XHOXKA Qa DA Network Nodes Edges 3 Quick Tour of Cytoscape When a network is loaded Cytoscape will look something like the image on the next page Cytoscape File Edit Data Select Layout Visualization Plugins Filters OD 4 He e e298 Cytoscape Desktop gt I PSPASHESXSOQXADE MA Network Node Edge 331 362 The main window has five components 1 The menu bar at the top See below for more information about each menu item 2 The too
21. 3 node4 and node5 as the targets respectively 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 allowed and indicate multiple edges between the same nodes For example the following specifies three edges between the same pair of nodes two of type pp and one of type pd nodel pp node2 nodel pp node2 nodel pd node2 Edges connecting a node to itself self edges are also allowed nodel pp 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 names nodes will be treated as identical nodes The name of each node will be the name in this file by default unless another string is mapped to display on the node using the visual mapper see 9 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 interaction type gt should be one of BP seated protein protein interaction So pene marae protein gt DNA e g transcription factor binding upstream of a regulating gen
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23. Cytoscape 2 1 User Manual Feb 2005 The Cytoscape Collaboration The Cytoscape project is an ongoing collaboration between e Po HE University of California at San Diego Institute for Systems Biology f j Memorial Sloan Kettering Cancer Center Institut pasiou Y a wees 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 Table of Contents UN AAA cecbaccanssbe ds snesveosesessluadecdeeseouseubeedeebaccestesuseacese 3 2 LAUNCHING CY TOSGADPE eneore teart ae as iE i i aE ses es iE E dose baecdscysbenasedesctecesees 3 3 QUICK TOUR OF CYTOSCAPE siecvsisesesk Rinsassceesuecniscsescoseusesevsnssiasesceassssasutes tots uanssvescebasacessvetesesveucdo sunueevseiaseaoee 5 4 COMMAND LINE ARGUMENTS AND PROPERTIES csssssssssssssssssscccssssccsececccesssscssenscesssssssscesecessees 10 5 BUILDING AND STORING INTERACTION NETWORKG ccssssssssssssssssessccccscsssscescescssssssccrecssesessssees 13 6 LOADING GENE EXPRESSION DATA cccccccscsssessscccsssssscenscccescsssscesecesessscsscesenscesesssscscececesssssssssenscessesssees 17 71 NODE AND EDGE ATTRIBUTES vicssssiessecocccssscssvecosncsccoesessecoucese dosveevocobuccascasvessenesaccdecesesuee csceecessosvessecoescssevs s 20 8 NAVIGA TION AND A
24. Di Visual Style A amp mes e KA x tm Pull Down Menu Network Node Edge 331 362 Nodes 331 0 selected Edges 362 0 selected Figure Using the Sample2 Visual Style Gene expression values are now displayed along a red green color gradient 9 2 Visual Attributes Graph Attributes and Visual Mappers The Cytoscape Visual Mapper has three core components visual attributes graph attributes and visual mappers e A visual attribute is any visual setting that can be applied to your network For example you can change all nodes to squares by setting the node shape visual attribute e A graph attribute is any 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 graph 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 includes a large number of visual attributes These are summarized in the tables below Visual Attributes Associated with Nodes Node Color Node Border Color Node Border Type The following options are available Node Shape The following options are available 0j mmoj oja TEA Node Size width and height of each node Node Label the text label for each node Node Font node font and
25. Graph button Apply to Graph Close You network should now show pd interactions in blue and pp interactions in red Sample screenshot is provided at right lt Nodes 80 0 selected 0 hidden Edges 66 0 selected 0 hidden 9 5 Tutorial Visualizing Expression Data on a Network The following tutorial demonstrates how to create a new continuous mapper The goal is to superpose gene expression data onto a network and to display gene expression values along a color gradient eS Set Visual Properties e Load a sample network From the main menu NodeArributes Edge Attributes Global Defaults select File gt Load gt Graph and select E a sampleData galFiltered sif Default e Load a sample set of expression data From the E Change Default main menu select File gt Load gt Expression Mapping Matrix File and select ColorGradient i sampleData galExpData pvals New Duplicate Rename Delete e Select Visualization gt Set Visual Properties SSS A E e Select New to create a new Visual Style Name Below Add Point your new style Sample4 Cai Equal e Click the Define button to define the newly C del 2 f created Visual Style Above e In the Set Visual Properties Dialog box select Node Attributes gt Node Color e Click the New button in the mapping panel e You will be prompted to select a mapping type passthrou
26. RG sig YHRO51W COX6 0 034 0 052 0 152 1 177 0 102 0 857 YHR124W NDT80 0 090 0 000 0 041 0 130 0 341 0 061 YKL181W PRS1 0 167 0 063 0 230 0 233 0 143 0 089 The first line is a header line giving the names of the experimental conditions Note that each condition is duplicated the first set of columns gives expression ratios and the second set gives significance values The significance columns can be omitted if your data doesn t include significance measures Every remaining row specifies the values for a gene starting with the formal name of the gene then a common name then the ratios then the significance values 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 COMMANDS Load an expression data file using the File menu of Cytoscape or by specifying the filename using the e option at the command line Mac OS X users who have downloaded the Mac OS X version of Cytoscape can also drag SIF and GML file to the Cytoscape application to load those files The x command line option indicates that the expression data should not be loaded into node attributes This is an advanced option and is typically only used when the number of expression conditions is sufficiently large that it becomes unwieldy in the nor
27. alization action for Cytoscape how your filter results should be displayed and pressing the Go button The Network Filter Feature The Network dialog is available from the Filters menu It allows you to create new networks and add remove nodes to from existing networks based on available filters The dialog box is shown below Network rire 00 Append ta ie Create new Network Filter List File Filter All Modes that match the selected Filter Available Filters with sigexp gt 1 0 interaction pd canonicalbame gallAC sigexp 0 0 ALIASES ALIASES pex de species sacc Edge interaction pp Add Nodes RemoveNodes The Attribute Browser Filter Feature The Attributes Browser if passed Filter item from the Data menu allows you to see the normal Cytoscape graph attribute browser for all nodes or edges that pass a given filter Select Layout Visualization Plugins Display attribute browser F5 Diff Attributes Browser if passed Filter Ctrl F5 Once clicked the following dialog box appears to allow you to choose an available filter Filter Br Selection ogc Available Filters wtR sigexp 1 0 interaction pd canonicalName gall A amp sigexp0 0 ALIASES species saco interaction pp Clicking on the Browser button will open the graph attributes browser The Diff Filter Feature The Diff featu
28. ally useful if there are multiple Cytoscape users all running in the same location using the same annotation a group of yeast biologists for example all within the same institute or if a group studies several organisms yeast human mouse The RMI server is a little bit of trouble to set up however and so many people will elect to use the in process server Building your own annotation files The annotation server requires that the gene annotations and associated ontology on controlled vocabulary terms follow a simple format This simple format was chosen because it is efficient to parse and easy to use The flat file formats are explained below The Ontology Format By example the Gene Ontology GO curator GO type all 0003673 0003674 0008435 0016172 0016173 0016209 0045174 0004362 0017019 Gene_Ontology molecular_function partof 0003673 anticoagulant isa 0003674 antifreeze isa 0003674 ice nucleation inhibitor isa 0016172 antioxidant isa 0003674 glutathione dehydrogenase ascorbate isa 0009491 0015038 0016209 0016672 glutathione reductase NADPH isa 0015038 0015933 0016209 0016654 myosin phosphatase catalyst partof 0017018 A second example KEGG pathway ontology cu 90 80 80 80 80 80 80 80 0 0 OS 0 OOO Ok ZO OBPNM WE FD O O C0 oO coc ao Oo 0 Ct Io ow i loo K ll A EGG type Metabolic Pathways etabolism Carbohydrate Metabolism
29. any later version you have the option of following the terms and conditions 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 mak xceptions 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 OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND OR P X T E OTHER PARTIE ROVIDE THE LIBRARY AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BU OT LIMITED TO TH PLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR URPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE BRARY IS WITH YOU SHOULD THE LIBRARY PROVE DEFECTIVE YOU ASSUME HE COST OF ALL NECESSARY SERVICING
30. cknowledges the following libraries 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 GNU Getopt in Java Information is available at http www urbanophile com arenn hacking download html Graph INterface librarY a k a GINY Information is available at http csbi sourceforge net JDOM Information is available at http www jdom org JUnit Information is available at http junit org JGoodies Looks Information is available at http www jgoodies com freeware looks index html Piccolo Information is available at http www cs umd edu hcil jazz Type Specific Collections Library from Sosnoski Software Solutions Inc Information is available at http www sosnoski com opensrc tclib Xerces Java XML parser Information is available at http xml apache org xerces j This product includes software developed by the Apache Software Foundation http www apache org This product includes software developed by the JDOM Project http www jdom org Appendix Annotation Server Format This section for advanced users Introduction Annotation in Cytoscape is stored as a set of ontologies e g the Gene Ontology a set of ontology controlled vocabulary term annotations for the genes from a given organism and a synonym table for gene names For example using the Gene Ontolo
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32. e Any text string will work but the above are the conventions that have been followed thus far Additional interaction types are also possible but not widely used e g Dala protein gt reaction PA reaction gt compound A compound gt reaction A genetic lethal relationship Die protein metabolite interaction MO ero metabolite protein interaction Even whole words or concatenated words may be used to define other types of relationships e g geneFusion cogInference pullsDown activates degrades inactivates inhibits phosphorylates upRegulates Delimiters Whitespace space or tab is used to delimit the names in the simple interactions file format However in some cases spaces are desired in a node name or edge type The standard is that if the file contains any tab characters then tabs are used to delimit the fields and spaces are considered part of the name If the 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 recognizes this extension when brow
33. e 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 although this name can be edited Pressing the Add Current Filter button will add your filter to the list of available filters to the left Numerical Filter Use Filters 000 Manage Filters Node Interactions Boolean Filter Topology Filter Numeric Filter String Filter Add current filter Remove selected filter Numeric Filter Select nodes or edges based on the value of numeric attributes Available Filters Filter Name Node gal1RG sigexp 0 0 Select graph objects of type Edge with a value for numeric attribute gallRG sigexp v gallRG sigexp a gal6R sam2exp that is 0 0 gal4RG sigexp Apia Available Actions gal3R sam2exp E gal2RG sigsig O Select Passed _ Hide Failed Go U list of Attrilgal2R sam2exp wtR sigexp The Numerical Filter also allows you to filter Nodes or Edges and presents you with a list of available attributes This filter matches greater than less than or equal to a number you type in the search box See the String filter description for more information 7 Use Filters ITA Manage Fi
34. e Cytoscape Visual Style feature you can easily customize the visual appearance of your network For example you can specify a default color and shape for all nodes use specific line types to indicate different types of interactions or visualize gene expression data using a color gradient All these features are available by selecting Visualization gt Set Visual Properties from the main menu or clicking on the color wheel in the main button bar menu 9 1 Introduction to Visual Styles The Cytoscape distribution you have downloaded includes three predefined visual styles to get you started To demonstrate these styles try out the following example e Load a sample network From the main menu select File gt Load gt Graph and select sampleData galFiltered sif e Load a sample set of expression data From the main menu select File gt Load gt Expression Matrix File and select sampleData galExpData pvals By default the Visual Style labeled default will be automatically applied to your network This default style has a blue background circular pink nodes and blue edges see sample screenshot below Cytoscape File Edit Data Select Layout Visualization Plugins Filters 3 e oe Cytoscape Desktop 1 d XO XAG ali Z E H A a Pull Down Menu Network Node Edge e Nodes 331 0 selected Edges 362 0 selected Figure Using the default Visual Style You can flip through di
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37. eName 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 or GML 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 regard 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 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
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39. er ipiToNPHash tester bioproc open bioproc txt w molfunc open molfunc txt w w cellcomp open cellcomp txt w bioproc write species s molfunc write species s r e cellcomp write species type Biological Process curator GO n species type Molecular Function curator GO n species s type Cellular Component curator GO n species So lines open associationFilename read split n sys stderr write found d lines n len lines 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 golDraw 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 s s has go term s tester printName golD if goOntology C cellcomp write S s Ss n printName golD elif goOntology P bioproc write s s n printName goID elif goOntology F molfunc write s s n printName golD Appendix GNU Lesser General Public License GNU LESSER GENERAL PUBLIC LICENSE Version 2 1 February 1999 Copyright C 1991 1999 Free Software Foundation Inc 59 Temple Place Suite 330 Boston MA 02111
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41. fferent visual styles by making a selection from the Visual Style pull down menu For example if you select Sample1 a new visual style will be applied to your network and you will see a green background and round blue nodes Additionally protein DNA interactions specified with the label pd are drawn with dashed edges whereas protein protein interactions specified with the label pp are drawn with drawn with a light yellow color which is difficult to discern on the green background see sample screenshot below The background can be changed through the Visualization menu f Cytoscape File Edit Data Select Layout Visualization Plugins Filters 008 Cytoscape Desktop ZA a Style Ad T t H AO XK BGS oo Men Network Node Edge 331 362 Nodes 331 0 selected Edges 362 0 selected Figure Using the Samplel Visual Style Protein Protein interactions solid lines are now distinguishable from Protein DNA interactions dashed lines 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 expression ratio and green represents a high expression ratio with thresholds set for the gallRGexp experiment bundled with Cytoscape in the sampleData galExpData pvals file See sample screenshot below r Cytoscape File Edit Data Select Layout Visualization Plugins Filters 4 e 060 Cytoscape Desktop ZA o Al
42. flatFilePrint id name isalDs partofIDs else badElements 1 print gt gt sys stderr no match to m2 print gt gt Ssys stdern E Se s SeecSeecee term print gt gt sys stderr goodElements d goodElements print gt gt sys stderr badElements d badElements Script 1 parseAssignmentsToFlatFileFromGoaProject py tools bin python 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 rawID find 1 return rawID bar A RP E SEE E O E ESA E E E ES O A ce O A O O ae A A aa ae Bath ot Gath ace def readGoaXrefFile filename lines open filename read split An 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 o print hash size d len ipiToNPHash print test map s gt NP_054861 Ss test
43. from a file which for convenience we usually call manifest ontology goOntology txt annotation 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 Obtain the GO ontology file Reformat it into the simpler flat file Cytoscape uses Obtain an annotation file we illustrate with yeast and human annotation Reformat the annotation files into the simple Cytoscape format TOARE 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
44. gh mapper discrete mapper or Apply to Graph Close continuous mapper for an overview of the differences between these mappers please refer back to section 8 2 Select continuous mapper and enter a descriptive name For example enter ColorGradient From the Map Attribute pull down menu select gall RGexp Click the Add Point button twice to add two data points Set the first point to 1 Below Yellow Equal White Set the second point to 2 Equal Red Above Black Click the Apply to Graph button 8008 Cyroscape 2 0 _ Users cerami temp cvsdirS cytoscape testData galriltered sif File Edit Data Select Layout Visualization Plugins Tools This visual mapper will set all nodes with a Abe e A OXA Ge gallRGexp value less than 1 to Yellow and rT a O HA J i all nodes with a gall RGExp value greater than 2 to Black Additionally all values between M El LN an T a 1 and 2 will be painted with a white red color os gradient Sample screenshot is shown at right F A RY P Y pes FR Ha E EA AN cn aja ay ri ANS L Sk DOI so Nodes 331 0 selected 0 hidden Edges 362 0 selected 0 hidden 10 Filters The Cytoscape Filter plugin which is packaged with the official Cytoscape 2 1 release and is active by default allows for a wide variety of fine tuned filtering on node and edge attributes loaded onto Cytoscape networks For example you can ea
45. gy the Saccharomyces Cerevisiae GAL4 gene s biological process is described as regulation of transcription to which GO has assigned the number 45449 a GO ID You can see below that regulation of transcription is a subcategory of transcription which is a subcategory of nucleobase nucleoside nucleotide and nucleic acid metabolism etc GO 8150 biological process GO 7582 physiological processes GO 8152 metabolism GO 6139 nucleobase nucleoside nucleotide and nucleic acid metabolism GO 6350 transcription GO 45449 regulation of transcription Cytoscape can use this hierarchical ontology to annotate recognized genes provided the user chooses a level of the hierarchy to use for a given set of annotations The ontology provided to Cytoscape does not have to be hierarchical but if it is not there is no real advantage to storing annotations this way compared to just storing the annotation terms in a node attribute file The annotation server originally called the biodata server is a Cytoscape feature which allows you to load navigate and assign annotation terms to nodes in a network There are two modes in which an annotation server can be run 1 As an in process version of the same code that runs in the same Java Virtual Machine as Cytoscape This is the default for the official release of Cytoscape 2 Asa separately running program an RMI server with which Cytoscape communicates The RMI server is especi
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47. ickness of edges etc These features are explored in depth in ie 9 change Backaraund Calar 08 Visual Styles section This menu also provides an Overview Bird s Set Visual Properties Eye view of your entire network which is helpful for navigating very Disable Visual Mapper large networks Plugins The PlugIns menu has menu entries or choices added by plugins that ETA Fitters E 7 have been loaded such as Find Enriched Attributes Find EntichedAtirib tes Filters This menu has been added by the plugin in the file filter jar The function of this plugin is not described further in this manual Additional menus may appear depending on the set of PlugIns you have chosen to load Help The Help menu allows users to launch the online help viewer and browse the table of contents Contents or view the help text associated witha Contents Fl context sensitive selection Context Sensitive By selecting Context Context eee EEE Sensitive menu item and then selecting a GUI component the help About related to the selected item is launched The About menu item displays information about the running version of Cytoscape The Network Management Window Cytoscape 2 1 allows 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 opt
48. ing 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 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 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
49. instance of Cytoscape See Commands Line Arguments and Properties for more information Data The Data menu allows you to display the attribute browser which HH Select Layout Visualization Plugins lets you view attributes assigned to both nodes and edges See HAIE Gane FS the section 7 Node and Edge Attributes Other options shown Diff Attributes Browser if passed Filter F5 relate to plugins which are packaged with Cytoscape 2 1 EJ Layout Visualization Plugins Filter Select i Mouse Drag Selects gt The Select menu contains methods and operations for selecting To New Network gt E Nod gt i nodes and edges and using the current selection to create a new ae network and an associated view z Select all nodes and edges SNA Deselect All Nodes and Edges LGA Layout Visualization Plugins Filte The Layout menu has an array of features for organizing the network Apply Spring Embedded Layout visually according to one of several algorithms aligning and rotating ad groups of nodes and adjusting the size of the network Most of these Shrink Graph feat ilable from plugins that kaged with C lei eatures are available from plugins that are packaged with Cytoscape Align 2 1 JGraph gt ISOM Radial Circle Spring Y yFiles Visualization The Visualization menu provides options for changing the mapping from biological data to a visual representation colors of nodes Plugins Filters H Overview th
50. ionally associated views can be organized hierarchically An example where a number of networks have been loaded and arranged hierarchically is shown below Cytoscape File Edit Data Select Layout Visualization Plugins Filters QD 4 197 Wed 1 606 Cytoscape Desktop gt Zt A LOX AG A a galFiltered gml gt child galFiltered sif galFiltered sif gfw 331 36 5566 331 331 Aa oo Nodes 36 0 selected Edges 42 0 selected The network manager marked by the red square 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 and 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 Since 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 five networks are loaded three green ones with views and two red ones
51. lbar 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 The network management window top left white box The overview window bottom left overview of the network 5 The main network view window which displays the network ed The Menus File HY Edit Data Select The File menu contains most basic file functionality File Load for loading a Load variety of file types File Save for saving File Help displays a credits screen AE File Print allows printing File Export As allows you to export to a file in a ae 5 number of graphics formats such as postscript File Exit closes all windows Bees POMS of Cytoscape and exits the program Exit SQ Edit The Edit menu contains a Squiggle feature that enables you to mark up Data Select Layout Visualiz your network This can be particularly useful during live presentations Squiggle gt Create View XV There are also options for creating and destroying views graphical Destroy aw AW representations of a network and networks the network data not yet Destroy Network OW visualized Destroy Selected Nodes Edges Preferences The Edit Menu also supports Preferences editing for properties and plug ins via a Preferences Dialog Preferences editing operates on the cytoscape props file associated with the user s
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53. ll now Node Attributes Edge Attributes Global Defaults see the main Visual Styles Properties dialog box shown at right Node Color Node Border Color Default _Change Default Mapping From this dialog box you can flip between Node Attributes Edge Attributes and Global Defaults You can also specify E default values for any visual property or define a new custom Ne Duplicate forename roaa mapping Create a new mapper For example to set the default node shape to triangles select Node Attributes gt Node Shape Then click the Change Default button and select the Triangle icon from the selection list Applying Changes to the Network To apply your visual style to your network hit the Apply to Graph Select the Apply button to apply button available in the bottom of the dialog panel ie es revised style to the graph Saving a Visual Style When you exit Cytoscape new visual styles or newly modified visual styles will automatically be saved in the vizmap props file You can therefore create a new visual style and apply it to all future networks 9 4 Tutorial Creating a New Visual Style with a Discrete Mapper e0e Set Visual Properties The following tutorial demonstrates how to create a new visual style with a discrete mapper The goal is to draw Protein DNA a T interactions with blue edges and Protein Protein interactions with Defa
54. lters Node Interactions Boolean Filter Topology Filter Numeric Filter String Filter Add current filter Remove selected filter Boolean Meta Filter Select nodes or edges based on a combination of other filters Available Filters Filter Name Boolean Filter ode canonicalName Select objects that pass ALL Y selected filters Node gal1RG sigexp lt 0 0 gal1RG sigexp lt 0 0 canonicalName Available Actions C Select Passed Hide Failed Go Update List of Filters Boolean Filter The Boolean filter allows you to define a new filter that is a logical combination of existing filters Available filters are displayed although the list can be refreshed by clicking the Update List of Filters button 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 Once created filters are saved for future sessions as long as you exit Cytoscape normally via the exit command in the File menu i e not via ctrl c on Linux Running filters Any available filter can be run by selecting a visu
55. mal user interface FOR EXAMPLE Load a sample gene expression data set using the menu File Load Expression Matrix File In the resulting file dialog box shown at right select the file sampleData galExpData pvals As described in the following sections Cytoscape is now ready to integrate these data with the underlying molecular interaction network Advanced Note the checkbox in the lower left corner of the file dialog asks whether to Copy Expression Data to Graph Attributes un checking this box has the same effect is as the command line option x and it is left checked by default If checked this means that expression data values will be stored internally in Cytoscape in two places once in an internal expression data object and once in node attributes The advantage of also storing this information on node attributes is that the expression information can be easily visualized Detailed file format Advanced users In all expression data files any whitespace spaces and or tabs is considered 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 see the section on name resolution in section 5 Building and Storing Interaction Networks The names given in the first column of the expression data file should match exactly the names used elsewhere i e in SIF or GML files The first
56. mple 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 The value class must implement the Serializable interface see the object serialization section of the Java tutorial allowing the data to be saved in an efficient binary form this binary attribute format is not directly supported by Cytoscape If the class is not a basic String or Number class it should have a String representation and a constructor that takes a String argument allowing Cytoscape to construct an instance from the String representation in the file If no class is 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 Every line past the first line identifies the name of an object and the String
57. n loaded and layout has been performed the network may be saved to and subsequently reloaded from GML format in future Cytoscape sessions Both SIF and GML are ASCII text files and you can edit and view them in a regular text editor Additionally GML is supported by some other network visualization tools SIF FORMAT The simple interactions 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 Cytoscape 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 relationship type gt nodeE nodeF nodeB nodeG nodeY lt relationship type gt nodeZ A more specific example is nodel typeA node2 node2 typeB node3 node4 node5 node0 The first line identifies two nodes called node1 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 node
58. ns The specification of plugins to be loaded into Cytoscape at startup time is also supported in cytoscape props and accessible in this dialog under the Plugins section In this special case the plugins property specifies a comma separated list of jar files or URLs to jar files containing plugins This Mo Cytoscape Preferences Editor Properties Property Name Value bioDataServer PleaseSpecify defaultSpeciesName PleaseSpecify secondaryViewThreshold 2000 viewThreshold 500 viewType tabbed Add Plugins Plugin Location plugins HierarchicalLayout jar plugins control jar plugins filter jar plugins yLayouts jar plugins yeast context jar Local 3 Add Note Changes to these properties and plugins will be saved on application exit and available on next start To use these new settings now please exit and restart Cytoscape property is parsed into its constituents and ES presented and managed in the Plugins table as at left Some common properties are described below Property name Default Valid values Related value command line argument defaultSpeciesName PleaseSpecify species names S this value must match the name in the species first line of the file specified in the bioDataServer s manifest for synonyms e g for yeast synonyms specify Saccharomyces cerevisiae bioDataServer PleaseSpecify annotation manifest and other manifest b file locations BDS viewThreshold 500 integers gt 0
59. oDialog suppressView Do not popup informational dialog when express file is vt VT lt view threshold gt Se the threshold of nodes at which views will not automatically be created project lt project file gt Specify the location of the project file script script lt script text gt endSpecify script text rp resourcePlugin lt resource plugins gt Specify the list of resource plugins Note that most data sets may also be loaded after Cytoscape is running See sections 5 Building and Storing Interaction Networks 6 Loading Gene Expression Data and 7 Node and Edge Attributes for details Additional command line arguments that are not recognized by the Cytoscape core are passed to the PlugIn modules Please refer to the documentation for each specific PlugIn for more details Cytoscape Properties The Cytoscape Preferences Dialog accessed via Edit gt Preferences has sections for general properties display editing and plugins specification via the properties mechanism Preferences in Cytoscape are stored in the form of Java properties specified in the cytoscape props file located in the users working directory home directory or Cytoscape distribution directory This file is automatically loaded at startup time and written upon normal exit of the application Cytoscape properties are displayed in the Properties section of the dialog These properties are configurable via Add Modify and Delete operatio
60. 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 fr 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 be combined with the library in order to run GNU LESSER GENERAL PUBLIC LICENSE ERMS AND CONDITIONS FOR COPYING DISTRIBUTION
61. re accessible from the Data menu shown above allows you to see which nodes or edges pass each of two selected filters and which nodes or edges those filters don t have in common i e it shows the differences between two filters This is useful for quickly comparing two filters You can then create a new network that contains the differences Create Network button or create a new filter that selects the differences Create Filter button DiffViewer 000 Networks Filters Filter 1 Filter 2 Available Filters Available Filters Node wtR sigexp gt 1 0 Vode wtR sigexp gt 1 0 Edge interaction pd Edge interaction pd Node canonicalName Node canonicalName Node gall1RG sigexp lt 0 0 Node gal1RC sigexp lt 0 0 Node ALIASES Node ALIASES Node ALIASES pex Node ALIASES pex Node species sacc Node species sacc Edge interaction pp Edge interaction pp Diff al diff 2 YGLO44C YGLO44c YER111 YER111C YKLIB82W YEKLIB2W YJRO19C YJRO19C YER110C YER110C YOL101C YOL101C YLR1 ATY YLR 1G iit bo Create Network Create Filter The same functionality is available here for networks You can select any two networks that are loaded and create a new network from their differences 11 Acknowledgements Cytoscape is built with a number of open source 3 party Java libraries The Cytoscape team gratefully a
62. rial Sloan Kettering Cancer Center Dr Chris Sander and the Institut Pasteur Dr Benno Schwikowski 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 Cytoscape also includes a number of other open source libraries which are detailed in Section 10 Acknowledgements below 2 Launching Cytoscape Currently Cytoscape runs under Java on Linux Windows and Mac OS X Although Cytoscape handles arbitrary types and sizes of interaction network it is most powerful when used in conjunction with large interaction data sets such as are currently available for species such as Saccharomyces cerevisiae budding yeast System requirements The system requirements for Cytoscape depend on the size of the networks the user wants to load view and manipulate We recommend a recent computer 1GHz CPU or higher with a high end graphics card and at least 256MB of free physical RAM Cytoscape expects a minimum screen resolution of 1024x768 1 Download and unpack the distribution Cytoscape is distributed as a compressed archive tar gz or zip containing the following files and directories cytoscape jar Main Cytoscape application Java archive cytoscape props User configurable properties and preferences vizmap props User config
63. rties Cytoscape recognizes a number of optional command line arguments including run time specification of network files and expression data g graph lt GML network filename gt xxx gml Loads a network file in GML format see 5 Building and Storing Interaction Networks i interaction lt SIF interactions filename gt yyy sif Loads a network file in SIF format see 5 Building and Storing Interaction Networks b BDS lt bioData directory gt e g annotation manifest Specifies which directory to use for the BioDataServer annotations e expression lt expression filename gt zzz pvals Loads an expression data file see 6 Loading Gene Expression Data n nodeAttributes lt nodeAttributes filename gt one or more Loads node attributes files see 7 Node and Edge Attributes j edgeAttributes lt edgeAttributes filename gt one or more Loads edge attributes files see 7 Node and Edge Attributes s species Set the default species name c noCanonicalization Turn off default node name canonicalization h help help help Help display these command line arguments p plugin JLD JLW JLL Specify a list of plugins jar files directories containing plugins URLs http to jar files or URLs to manifest files listing jar files props lt properties file gt specify and load a properties file headless noView Run in headless mode do not create and display the GUI n
64. s which allows you to filter nodes based on the edges that they are connected to Boolean which allows you to combine filters together using AND OR and XOR operators Topology which allows you to filter nodes based on the number of edges to other nodes Numerical which allows for gt and lt filtering operations on numerical attributes and String which allows for filtering using and as wildcards The Purple Box An existing or newly created filter can be edited in this area Each filter type has its own user interface for editing The Orange Box All available filters are shown in this list Initially this list will contain sample filters but as you create more they will be added here The Cyan Box Pressing Add Current Filter adds the filter being edited to the Available Filters box and Remove Selected Filter deletes the currently selected filter The Green Box This area contains default actions for a given filter These specify how Cytoscape should display the network components nodes and edges that pass a filter You can choose to have Cytoscape select the nodes and or edges that pass a given filter or alternatively have Cytoscape hide the nodes and or edges that do not pass a given filter A useful operation is to have a filter select a set of nodes and then send these nodes to a new network through the Select menu Creating Filters The important thing to realize when creating a filter is that
65. s 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 researchers when talking about that gene 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 simply 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 section Appendix Annotation Server Format 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 what set of names are the canonical names For example in budding yeast the ORF names are commonl
66. sily select all the nodes whose name contains a specific pattern that you define Example filters are shipped with the plugin to get started Base filters only operate on String and Scalar data i e any names descriptions or numerical node or edge attributes can be filtered A Boolean filter is also available that can be used to combine any number of existing filters in logical combinations so as you add filters the plugin becomes more powerful Using the Plugin If the Filter plugin is loaded then you should see a menu called Filters and the filter icon SE Use Filters F7 3 Sarai ess Network F Activate the filters using either the Use Filters menu entry or the large filters icon red and green arrows The filters dialog looks like the following without the colors Use Filters 1010 Manage Filters 3 Add current filter Remove selected filter i Available Filters Node Interactions Boolean Filter Topology Filter Numeric Filter String Filter pip p p di page Filter Name Nodelnteraction Select nodes which are the source w of at least one edge whith ode canonicalName w Available Actions P C Select Passed Hide Failed Go er Update List of Filters As for the colors The Red Box Each available filter has its own tab The default filter is Node Interaction
67. sing 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 fmi 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 Colors and other visual attribute defined in the GML file are not currently honored by Cytoscape only the node labels and layout information COMMANDS Load and save network files using the File menu of Cytoscape Network files may also be loaded directly from the command line using the i SIF format or g GML format options FOR EXAMPLE To load a sample molecular interaction network in MEN Edit Data Select Layout Visualization Plugi SIF format use the menu File Load Graph In Graph the resulting file dialog box select the file Help Node Attributes SampleData galFiltered sif After a few seconds a print m SS Expression Matrix File E Export As P Bio pata Server ECO small network of 331 nodes should appear in the main window To load the same interaction network as a GML use the menu File Load Graph again In the resulting file dialog box select the file sampleData galFiltered gml Node and edge attribute files as
68. sssscesececeeseseceeececceneuesuececececsesasececececeeeassceeececsesesasaeeeeeesenenaaeees 43 APPENDIX GNU LESSER GENERAL PUBLIC LICENSE ccoocnoonoonnconoocnnonnnonnnonononncnnncnnncanonnncnnocanocnnconnconaoonnoss 48 1 Introduction Cytoscape is an open source community software project for integrating biomolecular interaction networks with high throughput expression data and other molecular states into a unified conceptual framework 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 A software Core provides basic functionality to layout and query the network to visually integrate the network with expression profiles phenotypes and other molecular states and to link the network to databases of functional annotations The Core is extensible through a straightforward plug in architecture allowing rapid development of additional computational analyses and features The central organizing metaphor of Cytoscape is a network graph with genes proteins and molecules represented as nodes and interactions represented as links i e edges between nodes Development Cytoscape is a collaborative project between the Institute for Systems Biology Dr Hamid Bolouri the University of California San Diego Dr Trey Ideker Memo
69. such as gene or protein expression levels Once loaded expression ratios levels may be visually superimposed on the network used in a filter to select a subset of nodes or used to identify active modules and subsystems via plugin analysis tools An expression data set can be loaded at any time but are only relevant once a network has been loaded FORMAT Gene expression ratios are specified over one or more experiments using a text file The file consists of a header and a number of space or tab delimited fields one line per gene with the following format GeneName CommonName ratiol ratio2 ratioN pvall pval2 pvalN Brackets indicate fields that are optional The first two fields are the systematic gene name followed by an optional common name Expression ratios are provided for each experiment optionally followed by a p value per experiment or other measure of the significance of each ratio i e whether the ratio represents a true change in expression according to some statistical model Significance values are generated by a variety of software packages for analyzing expression data generated by DNA microarrays for instance a program VERA from the Institute of Systems Biology nttp www systemsbiology org VERAandsam A list of other microarray analysis packages is available at http www nslij genetics org microarray soft html Example GENE DESCRIPT gallRG sig gal2RG sig gal3RG sig gallRG sig gal2RG sig gal3
70. this section has the sole purpose of protecting the integrity of the free software distribution system which is implemented by public license practices Many people have mad 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 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 th original copyright holder who places the Library under this License may add an explicit geographical distribution limitation excluding those countries so that distribution is 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
71. ttributes as directional so note that 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 files use the same format Node attribute file names often use the suffix noa while edge attribute file names use the suffix eda Cytoscape recognizes these suffixes when browsing for attribute files Node and edge attributes may be loaded at the command line using the n and options or via the File Load menu When expression data is loaded using an expression matrix file See 6 Loading Gene Expression Data it is automatically copied into the Node Attributes data structure unless explicitly specified not to 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 category attributeCategory The first field is always the attribute name it cannot contain spaces The file may optionally include either of the class and category fields The category if present is saved and can be used by Cytoscape tools and plugins to group or filter the set of available attributes If present the class field defines the formal package qualified name of the class of the attribute values For exa
72. ult Node Attributes Edge Attributes Global Defaults red edges Change Default ii Mapping InteractionTypeColor B e Load a sample network From the main menu select File gt Load gt Graph and select sampleData galFiltered sif A E ee e Select Visualization gt Set Visual Properties aani e Select New to create a new Visual Style Name your new style Sample3 Seed Mapping with Random Colors e Click the Define button to define the newly created Visual Style e Inthe Set Visual Properties Dialog box select Edge Attributes gt Edge Color e Click the New button in the mapping panel e You will be prompted to select a mapping type passthrough mapper discrete mapper or continuous mapper for an overview of the differences between these mappers please refer back to section 8 2 Select discrete mapper and enter a descriptive name For example enter InteractionTypeColor e From the Map Attribute pull down menu select interaction You should now see two buttons one for pd Protein DNA interactions and one for pp Protein Protein interactions 4 cc 23 e Click the p d button and select a blue 100 0 Cytoscape 2 0 _ Users cerami temp cvsdir5 cytoscape testData sample 1 sif color File Edit Data Select Layout Visualization Plugins Tools e Click the pp button and select a red Sarthe LOXKAGe D color n e Click the Apply to
73. urable visual mapping preferences cytoscape sh Script to run Cytoscape from command line Linux Mac OS X cytoscape bat Script to run Cytoscape Windows LICENSE txt Cytoscape GNU License Cytoscape2_1Manual pdf Cytoscape 2 1 Manual the document you are reading now sampleData galFiltered gml Sample molecular interaction network file galFiltered sif Identical network in Simple Interaction Format galExpData pvals Sample gene expression matrix file BINDyeast sif Network of all yeast protein protein interactions in the BIND database as of July 2004 BINDhuman sif Network of all human protein protein interactions in the BIND database as of July 2004 yeastHighQuality sif Sample molecular interaction network file annotation Directory containing Gene Ontology database entries currently for yeast only Info in this directory is used to associate gene names with synonyms as well as process function and cellular location data plugins Directory containing cytoscape Pluglns in jar format From Ideker et al Science 292 929 2001 Obtained from data hosted at http www blueprint org bind bind_downloads html From von Mering et al Nature 417 399 2002 and Lee et al Science 298 799 2002 2 If necessary install Java If not already installed on your computer download and install the Java 2 Runtime Environment version 1 4 2 or higher It can be found at http java sun com
74. use and rat proteomes The second sample contains biological process annotation and each protein is identified by its NP RefSeq number These two naming systems IPI and RefSeq are two of many that you can use for 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 such single simple standard See section 5 Building and Storing Interaction Networks for more information The solution for those working with human genes or proteins is once you have downloaded the annotations file to Decide which naming system you want to use 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 Examine xrefs goa to figure out which column contains the names you wish to use 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 N Re ll Here are a few sample lines from xrefs goa SP 000115 IPI00010348 ENSP00000222219 NP_001366 BAA28623 AAC77366 AAC35751 AAC39852 BAB55598 AAB51172 AAH10419 2960 DNASE2 1777 DNASE2 SP 000116 IPI00010349 ENSP 00000324567 ENSP00000264167 NP_00365
75. well as expression data and extra annotation can be loaded as well 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 also represents its corresponding protein Nodes may also be used to represent compounds and reactions or anything else instead of genes If a network of genes or proteins is to be integrated with Gene Ontology GO annotation or gene expression data the gene names must exactly match the systematic ORF 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 Cytoscape 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 source
76. without views 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 Select gt To 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 The available network views are also shown as tabs on the top of the view window You can click on the tab to go to the named network and the network manager will update accordingly Advanced users Cytoscape also has two viewing modes that alter the way in which these windows are displayed This mode can only be selected on startup of the program by adding the option on the command line see section 4 Command Line Arguments 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 This feature can be turned on an off via the Visualization menu The red outlined blue rectangle in the overview window shown below can be dragged with the mouse to navigate to a part of the network The size of the navigation rectangle depends on the size of the active view and the zoom level of the view The rectangle is smaller if the view is zoomed in and larger if zoomed out eee 4 Command Line Arguments and Prope
77. y used as the canonical names 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 be preserved This conversion of names to a common set allows Cytoscape 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 s option or by adding a line to the cytoscape props file of the form defaultSpeciesName Saccharomyces cerevisia The automatic canonicalization of names can be turned off with the c command line argument i e java jar cytoscape jar c or by not loading any annotation This canonicalization 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 6 Loading Gene Expression Data Interaction networks are certainly useful as stand alone models However they are most powerful for answering scientific questions when integrated with further information about the biology associated with the network

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