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VAMP Administration and User Manual

1. A Cancer16 3 A Cancer 73 A Cancer 8 3 Related Arrays A Cancer25 3 A Cancer26 3 A Cancer27 3 A Cancer28 3 A Cancer29 3 A Cancer 3 A Cancer30 3 A_Cancer313 A Cancer323 A Canccr33 3 A Cancer34 3 A Cancer35 3 A Cancer35 3 A Cancer37 3 Open dialog the FrAGL dialog box Based on Ratio Probe status is defined with the Color Legend thresholds NormalMin Nor malMax and Amplicon see Figures 3 24 Based on Status Probe status is defined with Gained Lost Color Codes GNL Type of alterations For gain region the user can search for either only Gain either only Amplicon or merge Gain and Amplicon Color bars ratio average Color bar corresponds to the ratio average of probes with the alteration Color bars confidences Color bar corresponds to the percentage of profiles without missing values Minimum support of alterations Probe with a frequency less than this number are dis carded Minimum value of confidence The confidence corresponds to the percentage of profiles without missing values Probe with a frequency which have been computed with less than this number are discarded Results The frequency is displayed in a profile view see Figures 3 36 or in a Karyotype classical view see Figures 9 13 Report The frequency are saved in a HTML or CSV file Fw ZC M f a ErAGL Dialog Erequency of Amplicon Gain and Loss Based on fe 4 Probe ststus is defined
2. 1 element Ser institutCurie MM cue i come 4 Figure 3 69 Visualizations of the results of Correlation Analysis From top to bottom corre lation coefficients p values FWER adjusted p values FDR adjusted p values All p values are plotted in og10 scale and given the sign of the corresponding correlation coefficient 54 Chapter 4 Analysis example Bladder Cancer 4 1 Introduction This scenario ab eege the g wil om to compare the amplified regions egal ze in three bladder cancer datasets Blaveri et al bons Stransky et all bood Veltman et al Veltman et al To run the interface you need to sis ai nod your Java Virtual Machine as explained e http bioinfo curie fr actudb Java configuration html At least 1Gb RAM memory is necessary on your computer 4 2 Import the genomic profiles First start the VAMP software La Rosa et all 12006 from the web page http bioinfo curie fr actudb access php Then load the array CGH profiles as follows 1 click on File Import see Figure 2 select all the profiles in the CGH ARRAYS blaveri_2005 Arrays directory see Figure 4 1 b Repeat the previous steps for the stransky_2006 directory and for the veltman_2003 directory in the veltman_2003 directory do not select the eight first normal array CGH profiles n b if you wish to import data from one specific chromosome choose Chromosome 6 select All arrays in th
3. 3 5388 Cancer Human douglas douglas L public Cancer 1 1 False RP11 383610 201807 724 0 404995 2 7 s24e49 0 44639 167 1985858083 Chr 4 Human 400 Cancer RF11 35D5 T35827 8 Figure 3 3 Info Panel left and Mini Map Panel right 14 The main frame see Figure 3 4 provides various ways of visualizing molecular profiles which are described in details in subsection 3 2 2 WAMP is developped and registered by f 0611 12 13 14 15 16 171219200122 E Y Human Institut Curie I we ii li WII miiy us 9 10 11 13 13 14 15 16 liana E Y 12 13 14 15 l 1712192022 X Y z 12 13 14 15 16 1718192022 K Y N 11 13 13 14 15 l 111214002 X Y Po AA Va Lei 9 10 11 12 13 14 15 16 I 15 152022 X Y bk 1 13 M 15 16 1719192022 E Y E 0 147 1 2 3 4 5 5 X 8 as vua isi BLAU oi NI die ir del s Eu 12 13 14 15 l 1712192002 X Y 10 12 13 14 15 16 171819200D2 Y Human istit M 3 Figure 3 4 Main frame Graphic Panel 3 2 Basic functions All user actions are accessible either through a Menu on the menu bar or through pointing to or clicking objects When using VAMP the session can be saved in local XML files Reloading the file later on allows the continuation of the analysis within the context of the previous work or allows the exchange of results and data with colleagues All user preferences can
4. lt Stage gt 2 lt Stage gt lt Location gt Left lt Location gt lt Bat26 gt Stable lt Bat26 gt lt ClinicalData gt lt SampleAdditionalData gt Note that any property specified by lt ClinicalData gt will be used in VAMP within functions related to Sample Annotation see section 3 3 6 In the example above the properties Age lt Sex gt lt Stage gt lt Location gt lt Bat26 gt were not previously known by VAMP but they will be taken into account by VAMP 12 Chapter 3 User Manual 3 1 Overview A typical VAMP window is divided into three areas figure B I the main frame consists of the graphical display of the profiles the top left frame controls zoom search and drawing options the bottom left frame offers the choice between textual information on the object under the mouse pointer or context information called MiniMap VAMP V1 3 15 Point View File Views Edit Tools Help Booming Search Arrays Search Elements Color Legend Y Range Point View B elements Chr 2 Human 400 Cancer1 HiniHap gi 5 6 7 8 9 1011 12 13 1415 16171819322 R Y Human 7 sve eur ti fot ime 3 4 5 6 7 amp 9 1011 12 13 14151617181 as m LL a PRA ee 3 4 5 6 7 8 9 10 11 12 13 4 15161718 ei a7 Bee een EA 2 3 4 5 6 7 amp 9 10 11 12 13 1415161718 m o el sis eo Eai 20 KT 5 4 5 6 7 T 9 1011 12 13 14151617181 a V a ER bob 5 4 35 6 7 9 10 11 12 13 14 15 1
5. 0 88 lt Signal gt lt PosBegin gt 13850 lt PosBegin gt lt PosEnd gt 14650 lt PosEnd gt lt Size gt 800 lt Size gt 19 lt Properties gt lt 0bj gt lt Obj gt lt Properties gt lt Type gt ProbeSet lt Type gt lt ObjectId gt IMAGE 190915 lt ObjectId gt lt Signal gt 0 03 lt Signal gt lt PosBegin gt 167764 lt PosBegin gt lt PosEnd gt 168564 lt PosEnd gt lt Size gt 800 lt Size gt lt Source gt IMAGE lt Source gt lt SourceID gt 190915 lt SourceID gt lt Properties gt lt 0bj gt lt Array gt lt ArraySet gt 6
6. 1 pps Light Green 2 eor en3 Light Pink 1 12 Light Pink 2 03 Other 04 D I A F lt i I d SE Fea ans Lr da Just eR ene E H Ge Ach m AT ud raa 06 08 10 12 Human 13 A Cancer 3 doa Figure 3 33 Customize Analysis Choose your favorite color 3 3 2 FrAGL Frequency of Amplicon Gain and Loss view The identification of systemic alterations within a set of tumors is central to the analysis of CGH array data for two reasons Firstly it can pinpoint new candidate genes as tumor suppressor genes and oncogenes are thought to be present in regions of loss and gain respectively Secondly some alterations may be significantly correlated with clinical phenotype and may therefore be useful for diagnosis and prognosis The simplest way to identify informative regions is to work at the probe level For each probe the fraction of tumors with gains and losses over the dataset is computed see Figures 2 34 and displayed in the FrAGL view see Figures 3 36 606 File Views Edit Tools Help 3 CGH Affy SNPs Transcriptome LOH ChIP chip Clustering Breakpoint Frequency Cytogenetic Banding Diffential Analysis Genome Alteration Signal Histogram Genome Annotation Sample Annotations Chromosome Switch Filter Sort by Misc f ey Chr 7 Human 400 400 A limlRR7 3 Figure 3 34 Tools FrAGL Compute 32 b registered by Institut Curie P VAMP is developped and E
7. 10 A HK28 10 A HK ZU D institutCurie 249 208 166 125 083 042 000 040 O81 123 144 206 247 288 330 371 Figure 3 60 Signal Histogram profiles Signal Histogram profiles view The values corre spond to the over the whole dataset from Patil et al 47 The aim of the differential analysis is to compare the signal value of each probe between two user defined groups of tumors The user has to perform the following steps e First the user must open a new double window see Figure 3 61 e Then the user load in the top panel the tumors defining the first group see Figure 3 62 e The tumors defining the second group are loaded the bottom panel see Figure 3 63 e Launch the analysis see Figure 3 64 eee VAMP V1 4 12 Point View File RUTA Edit Tools Help New View d AMP i ed and Current View HSN ie Specialized View k Barplot View Curve View List View DotPlot View zooming Search Arrays b Point View Figure 3 61 Views New View Double View Point View First the user must open a new double window 0406 VAMP V1 4 12 Point View Sita Views Edit Tools Help Save View d em VAMP is developped and Load View registered by Institut Curie Export in Top Panel Update in Bottom Panel Configuration Print Close Human A Cancer 3 iris A Ccerl 3 13 00 1 2 Hum sen Figure 3 62 File Import in Top Panel Then the user must loa
8. 3 47 d Simple View Double View Specialized View VAMP V1 3 15 Point View Point View Barplot View Curve View k h h List View DotPlot View 19 The Karyotype View see Figures and 3 13 displays profiles with the classical CGH rendering vertical representations of chromosomes with cytogenetic banding and contiguous representation of sample profiles VAMP V1 3 15 Point View Slee File Views Edit Tools Help Point View Barplot View Curve View gt Simple View Current View NM Double View b x Specialized View P List View DotPlot View Karyotype Classic View Figure 3 12 Views Simple View Karyotype Classic View The user opens a new Karyotype Classic View VAMP V1 3 15 Karyotype Classic View Ea lx File Views Edit Tools Help VAMP is developped and registered by Institut Curie Search Elements Color Legend Y Range Put landmark and center GH Array Merge Chr 1 Array H Pin up info Booming 4 Search Berays Put landmark Put begin landmark Karyotype Classic View Edit properties 24 elements V S Copy ID in search panel CGH Array Merge Chr 3 Cancer10 n Clone Count 204 Cancer11 Date Thu Apr 16 14 33 SS Cancer12 GenomicinstabilitiType CH Cancer13 Name Chr 3 Array HbRep 3 NbSpot 8388 Cancer 15 Cancer14 HumHista Cancer Cancer 16 Organism Human Cancer17 Project douglas I Cancer 18 Projectld douglas Ratio S
9. 6 20510376 20601920 91544 7 NM 001343 CTD 2018P8 null 6 20501182 271 E2F3 e 20510376 20601920 91544 7 INM 001343 Clone Gene Name Nmc Chr Position Size Ratio GeneSymbol Chr GeneBegin GeneEnd Size Strand NbExons jmRNA ID CDKAL1 6 20642666 21339743 697077 16 NM_017774 RP11 3D15 null 6 21715614 ES ES 6 21701950 21706826 4876 1 INM_003107 RP11 273J1 null B 22030456 181700 Clone Gene Name mc che Position_ siz_ Ratio GeneSymbot chr GeneBegin GeneEnd sire Strand NbExons mRNA ID RP11 273J01 null 6 22178710 341 Clone Gene Name Nmc Chr Position Size Ratio GeneSymbol Chr GeneBegin GeneEnd Size Strand NbExons mRNA ID RP11 208E21 null 8 100717687 140632 0 2035 VPS13B 8 100094669 100358383 864314 62 HM 017890 COX6C 8 100959547 100975071 15524 4 NM_004374 RP11 102K7 null 8 101238461 179185 RGS22 8 101042452 101187520 145068 28 NM 0156868 RP11 102K7 null 8 H si 8 101214763 101226853 1203D 5 NM_001029860 ivi Termin Figure 4 9 Gene list 60 In the previous part the minimal amplified regions have been identified and the gene list retrieved In 2006 transcriptome have been studied and these data can be used to identify among the gene list the genes which show a significant correlation with respect to DNA copy number alterations This will be detailed in what follows l open a new view Views New View Simple View Point Vie
10. Analysis Chromosome M Chr 1 2 3 4 5 6 7 8 9 10 11 12 1 Clone Count 2984 Date Thu Apr 12 11 42 01 2007 Name ANADIFF 114152 Organism Human Pvalue 1 0 Pvalue Correction None Ratio Scale L Test Student Use Sign PP 1 2 3 4 5 6 7 8 9 10 11 12 13 141516171812 22 X Y Human Minimap institutCurie Dro dejo uus E Figure 3 66 Differential Analysis protiles Differential Analysis view ol Correlation Analysis aims at quantifying the overall influence of DNA copy number changes on gene expression gene dosage effect using paired copy number and expression microarray measurements Details on the algorithm and its implementation are given in the poster we presented at ISMB 2007 Calculating correlations Assuming that such paired profiles have been loaded within VAMP see section MA for an example the analysis can be launched from the menu Tools Correlation Analysis Compute 2 e CA Correlation Analysis Dialog CT CA Correlation Analysis Dialog Scope 2 All Criteria Ratio fl Smoothing Correlation fe Pearson Spearman Results ei Correlation coefficient O p value des FWER whole genome FWER by Chromosome FDR whole genome L de de FDR by Chromosome OK 1 k Cancel Figure 3 67 Compute Dialog for Correlation Analysis Several parameters can be chosen to run a Correlation Analysis scope should correlation coefficients be calculated on all data or
11. EB AA BA DL eS ee lt q ss FASS rSn pue wu Pilze F EEN DAT set Bil ds As gib sr CH _ AR Hoominqg Search Search Arrays E keng pra dr Ra Uu IL ll AA EM UA ae i Search Elements 4 wam A Lolor Legend QT Range Wu d u y I I Wi kmit r O dei Eag Ziffer Craft e HE perm ug 8 mies ni ech PARAS ee esa Po ae ee oC ot Dot Plot wiew Er Ohn FS rr beer Kirch rea Bees a Ll Eer Les tat hey lege len EE 26 elements mp RO ow f E Med e bt E ace ui on mr B rbel u wasi CGH Chromosome Merge pm DES GESITT wazi bunt ep Win SSH PE as TTA imi Chr 1234567 i t e s la Ki aQ aile Clone Count 2706 Ben Te A bai d Ki gl E ml pele BLU SS pa EE mms pum CH e Date Thu Apr 7 1 L FM w q AA PS RN ep opum wm E m parm es 3 GenomiclnstabilityTwpe CH e wm 0 mm mmmg Li EE mb umm ma Hame Lancer j hl il wem wii T GGG EE GE EE E CC ON LH NbRep UG cR OSO E 1313140 2817129032034 NbSpot odo 3 4 5 6 T 8 9 1011 12 131415050 712 2572 24 7 BLS r il Info HiniMap M uli ars t Figure 3 15 Dot Plot View Al This view see Figure 3 16 lists the names of all the arrays currently loaded and can be used for selecting or keeping track of the data under study VAMP V1 3 15 Point View File Views Edit Tools Help New View ill vamo is developped Current View k Point View Barplot View L Curve View III DIE DotPlot View cc Sees Gained Lost Color Cod
12. K J So S Fan S T Kakar S Furge K A Buttner R and Chen X 2005 Array based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for So gain in hepatocellular carcinoma Carcinogenesis 26 2050 2057 Pollack J R Sorlie T Perou C M Rees C A Jeffrey S S Lonning P E Tibshirani R Botstein D Borresen Dale A L and Brown P O 2002 Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors Proc Natl Acad Sci U S A 99 12963 12968 Rouveirol C Stransky N Hup P La Rosa P Viara E Barillot E and Radvanyi F 2006 Computation of recurrent minimal genomic alterations from CGH data Bioinfor matics 22 0 11111C11C A A LLUCY D Ivllllulo IN VD D L IWLVYALTILUO A 1 ALCL J Liblla D LUCO J I Gray J W Jain A N Pinkel D and Albertson D G 2001 Assembly of microarrays for genome wide measurement of DNA copy number Nat Genet 29 263 4 Snijders A M Schmidt B L Fridlyand J Dekker N Pinkel D Jordan R C K and Albertson D G 2005 Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma Oncogene 24 4232 4242 Stransky N Vallot C Reyal F Bernard Pierrot I de Medina S G D Segraves R de Rycke Y Elvin P Cass
13. also be 15 LO ally OCT WIMQOW HUE 1C11C1CllllS VOLIS aubOlllabilally adapted C S OUT d GOL DIOU VIEW LO a karyotype view An advanced printing function is offered see 2 2 5 for details 3 2 1 Data import Once XML array files and import files have been generated see DZ data can be imported into VAMP as shown in figure 3 5 After selecting a project figure 3 6 the user can import either pan genomic profiles 3 7 or chromosome profiles 8 8 for the same project or from different projects ee VAMP V1 4 12 SUR Views Edit Tools Help Save View i MP is developped anc Load View Jistered by Institut Cu Export Figure 3 5 Import data Ce n n VAMP Import Data L VAMP Data P CGH ARRAYS Le LA REPLICATION TIMING T GENOME ANNOTATIONS Import data Cancel Refresh i r A Figure 3 6 Select a project 16 ue VAMP Lata Y J CGH ARRAYS P gt blaveri 2005 P bredel 2005 Y douglas 2004 Y Arrays A Cance r20 3 L A rCanrar21 3 L2 38 33 L2 L9 9 DL LP L Figure 3 7 Import pan genomic profiles ODO VAMP Import Data d VAMP Data Y CGH ARRAYS P blaveri 2005 P bredel 2005 Y I douglas 2004 P 3 Arrays Y 7 Chromosomes Y L3 chro1 All arrays d F d i o i ERE j 4 1 n A B Bip L2 I2 L2 L2 LALA Figure 3 8 Import chromosome profiles p VAMP currently offers several types of visualization that can be displ
14. cgh jpg gt lt GraphElementIcon type CGH Average url file C VAMP images vamp cgh jpg gt lt GraphElementIcon type Transcriptome url file C VAMP images trs jpg gt lt GraphElementIcon type Transcriptome Average url file C VAMP images trs jpg gt lt GraphElementIcon type Transcriptome Relative url file C VAMP images trs jpg gt lt GraphElementIcon type Transcriptome Merge Relative url file C VAMP images trs jpg gt lt GraphElementIcon type LOH url VAMP images LOH jpg gt indicates the physical localization of cytogenetics descriptions lt Cytoband organism Human url file C VAMP data xml cytoband human mai_2004 resolutions 400 550 850 default_resolution 400 gt lt Cytoband organism Mouse url file C VAMP data xm1 cytoband mouse resolutions 400 indicates the physical localization of a file used for customized printing of a reporting lt PrintPageTemplate url file C VAMP configuration xml print report xml gt 8 2 Sample user configuration XML file lt xml version 1 0 encoding iso 8859 1 gt lt CGHConfig gt lt AxisBG gt ORANGE lt AxisBG gt lt AxisEastSize gt 40 lt AxisEastSize gt lt AxisFG gt BLACK lt AxisFG gt lt AxisKaryoDisplayerFont gt MonoSpaced PLAIN 8 lt AxisKaryoDisplayerFont gt lt AxisKaryoNameDisplayerFont gt Serif BOLD 9 lt AxisKaryoNameDisplayerFont gt lt AxisKaryoSmallDisplayerFont gt MonoSpaced BO
15. click on File Import see Figure 5 1 a 2 select all the profiles in the CGH ARRAYS douglas_2004 Arrays directory see Figure 5 1 b n b if you wish to import data from one specific chromosome select CGH ARRAYS douglas_2004 Chromosomes chr see Figure 5 1 c Save View Load View Export Import LI att Configuration gt Print b Close a File menu b Genome wide c Chromosome pro profile import file import optional Figure 5 1 Import Data The genomic profiles are displayed in the interface as shown in Figure 63 Search Arrays Search Elements Color Legend Y Range Point View 85 elements CGH Chromosome Merge 1 2 3 4 5 GenomicinstabilityType CIN ImgSoftware NA Bn A E EE EEE Mee o o b ob D b b b ib b b b e e D b m b t mte ma x s x s E EORUM RR NNNM AS 259252239 ZAS EE w P 4X1 VIA R40 110 EE 2 pias E T Bi Ty a TT TT ee a A i 2 ee eee INE p Eum ee ee ees esst L pb le FER rin a e DE EE LO IE EA E El EEN TEE PTET LN A eat ee E Tee 5 y E 46 3 E 1116 t15 et8 318 t29 55 3 0 3 it 3 3 2 3 E k 3 3 H co10 3 a3 5 3 H Figure 5 2 Array CGH profiles Open a new view see Figure 5 3 and repeat the previous steps for the nakao_2004 directory D Edit Tools Help New
16. following example the user widened the visible range so that all amplicons are dis played ae Z 1 2 3 4 5 6 7 8 91011 1 13141161789 2 X Y Human Point View 1 alament a Chr1 Human 400 400 Cancer18 mn ES pos 2 gi E EERE REESE CERRSSSS ER CECE SEGEMEEERR SE 43 2 3 4 5 6 23 9100 0030515890 X Y BREE Le E ER DE TS ee ee or ELE BT ES 1 2 3 4 5 6 7 8 91011 123H1516171890P2 X Y Human institutCurie ege eeh th x 7A Figure 3 27 Y Range Panel 3 2 5 Print An advanced printing function is offered either in visible mode only the profiles that are visible on the screen are printed or in global mode all profiles in the view are printed A template is offered for defining the output of the printing this can for example include several frames in an arbitrary composition to which text or images can be added It can be used for defining and printing standardized outputs The user can also interactively monitor the print preferences In any case the print function is WYSIWYG through an intermediate preview which can be edited by the user The print menu File Print Standard Report Template opens the default printing template see Figure 3 28 and allows the user to print or export into PNG format VAMP Print Previewer ii SGS File Edit Contents Templates Grid er n en Lh Cancerll Thu Apr 7 16 14 33 2005 8 9 WH 12 13 HM 151617181922
17. only on selected regions if any criteria should correlation coefficients be calculated from copy number ratios or from smoothed copy number values given by GLAD correlation which type of correlation coefficient should be used The Pearson correlation coef ficient measures the extent to which the association between copy number and expression is linear its sensitivity to outliers makes it suitable to detect associations within regions that are amplified in only few samples The Spearman correlation coefficient is the Pear son coefficient between measurements ranks it is therefore robust to outliers and able to detect non linear associations 02 The last parameter in Figure allows to choose which results should be displayed The choice may be made before the analysis is launched but it can also be modified without further calculations after the analysis from the menu Tools Correlation Analysis Redisplay DO GT CA Correlation Analysis Redisplay GT CA Correlation Analysis Redisplay Results fe Correlation coefficient O p value FWER whole genome FWER by Chromosome FDR whole genome 010 FDR by Chromosome 17 L OK 3 Cancel Figure 3 68 Tools Correlation Analysis Redisplay Correlation Analysis Redis play dialog The Redisplay dialog proposes several options correlation coefficient default Pearson or Spearman correlation coefficient depending on the ch
18. the clones the transcriptome probes SNPs User configuration It is possible to customize the visual rendering of VAMP The top left panel provides a user friendly interface for customizing the most important visual features see section 3 2 4 Once the user has chosen his favorite parameters he can save his configuration into an XML file using File Configuration Save see Figure 2 1 Any saved configuration can be restored using File Configuration Load This XML configuration files also stores features that cannot be accessed directly within VAMP menus To modify such features just edit the XML configuration file For example if you change line lt CanvasBG gt ccccff lt CanvasBG gt to lt CanvasBG gt GREY lt CanvasBG gt the main frame background color will switch from light blue to grey A sample user configuration file is given in the Annexes see 8 2 VIEWS cait 10015 Help Save View kr MP is E Load View Ustereg by Institut Cu Export Import Update liris l Load Print d Save Close Restore Factory Default Figure 2 1 File Configuration Save 2 2 4 Data format The data format which is used in VAMP is XML eXtensive Markup Language Two types of XML file are necessary to run VAMP e Array files which contain the information related to a molecular profile for each experi ment there is a file which stores both array level information e g patient ID number of clone
19. with the Color e Ratio thresholds NormalMin NormalMax and Amp O Status Gained Lost Color Codes GNL Types of alterations M Gain Amplicon f Gain m Amplicon Merge Gain Amplicon M Loss Color bars e 4 color bar the io average Use ratio average of probes with the alteration color bar corresponds to the percentage f Use confidence OF profiles without misting value Minimum support of alterations f Number 1 L i 28 Percent Minimum value of confidence Ze pcoctios witha el f Number 1 ES 28 C Percent Results Y Display Y Profile Karyotype Report HTML report _ CSV report Report Details OK Cancel Figure 3 35 FrAGL dialog Different FrAGL options are available 99 i l H H d H H n li m E WM m WU Wiper F T Figure 3 36 FraGL profiles FrAGL Frequency of Amplicon Gain and Loss view The values correspond to the percentage of gained and lost clones identified with GLAD over the whole dataset from 2003 3 3 3 Finding common alterations among a collection of CGH array profiles Instead of looking for individual probes carrying genome alterations it is often fruitful to con sider the geography of the genome and to look for whole regions 2006 have described algorithms for finding common alterations Two algorithms are proposed within VAMP It is necessary that breakpoints gain loss and amplicon regions have been previously de
20. 031 xml lt Item label gm13330 url public all chr02 gm13330 xml lt Folder gt lt Folder label chr03 type CHR gt lt Item label All arrays url public snijders chr chr03 xm1 lt Item label gm00143 url public al1 chr03 gm00143 xm1 gt lt Item label gm01524 url public al1 chr03 gm01524 xm1 gt lt Item label gm13031 url public al1 chr03 gm13031 xm1 gt lt Item label gm13330 url public all chr03 gm13330 xml lt Folder gt lt Folder gt 14 lt FolderSet gt 8 4 CGH array XML file lt xml version 1 0 encoding iso 8859 1 7 lt ArraySet gt lt SetName gt gm01535 lt SetName gt lt Array gt lt Team gt public lt Team gt lt Organism gt Human lt Organism gt lt Project gt snijders lt Project gt lt ProjectId gt 15 lt ProjectId gt lt NumHisto gt 4948 lt NumHisto gt lt SampleAdditionalData URL additional snijders gm01535 xm1 gt lt Chr gt 1 lt Chr gt lt Name gt gm01535 lt Name gt lt Date gt Thu Apr 7 16 14 54 2005 lt Date gt lt Type gt CGH lt Type gt lt 0bjKey gt Name lt ObjKey gt lt NbSpot gt 6813 lt NbSpot gt lt NbRep gt 3 lt NbRep gt lt RatioScale gt L lt RatioScale gt XUrl public all chr01 gm01535 xml Url lt NbObj gt 2271 lt NbObj gt lt Obj gt lt Properties gt lt Type gt Clone lt Type gt lt Y gt NA lt Y gt lt X gt 1000 lt X gt lt Chr gt 1 lt Chr gt lt Name gt GS1 232B23 lt Name gt lt Smt gt NA lt
21. 19202122 X Y Human 67 Chapter 6 Availability VAMP is available upon request to It can be tested on public data sets at the following url http bioinfo curie fr vamp VAMP is also integrated into CAPweb a complete bioinformatics pipeline for array CGH data analysis CAPweb can be tested at the following url http bioinfo curie fr CAPweb Note that some movies present as well the main functions of VAMP for basic functions data Analysis synteny analysis http bioinfo curie fr vamp doc 68 Chapter 7 How to cite us If you used VAMP please cite us as follows La Rosa et al 2006 VAMP Visualization and Analysis of CGH arrays transcriptome and other Molecular Profiles Bioinformatics 22 2066 73 69 Bibliography Blaveri E Brewer J L Roydasgupta R Fridlyand J DeVries S Koppie T Pejavar S Mehta K Carroll P Simko J P and Waldman F M 2005 Bladder cancer stage and outcome by array based comparative genomic hybridization Clin Cancer Res 11 7012 7022 de Leeuw R J Davies J J Rosenwald A Bebb G Gascoyne R D Dyer M J S Staudt L M Martinez Climent J A and Lam W L 2004 Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes Hum Mol Genet 13 1827 1837 Douglas E J Fiegler H Rowan A Halford S Bicknell D C Bodmer W Tomlinson I P M and Carter N P 2004 Array comparative genom
22. 32 ATIRP11 159C8 FdrBc 5 97 FdrWg 5 97 FwerBc 5 52 FwerWg 5 52 NA False Objectid 41632_AT Position 20510376 Pvalue 9 53 Ratio 0 888 91548 SS Y r c H ee VF I Hy o 10672000 21344000 32016000 42688000 53360000 44032000 74704000 85376000 96048000 106720000 117392000128064000 1387346000 149408000 160030000 000 VAMP V1 4 35 GTCA File Views Edit Tools Help VAMP is developped and ee registered by Institut Curie O 10672000 21344000 32016000 42688000 53360000 64032000 74704000 85376000 96048000 106720000 117392000129064000138734000149408000160080000 01155 SE H 93 90 87 BA SI 738 as 72 69 institutCurie ea 1 element 400 4 Chr 6 Human 400 CTCA 011558 41632 AT 20544995 000 VAMP V1 4 35 GTCA File Views Edit Tools Help VAMP is developped and registered by Institut Curie a 10672000 21344000 32016000 42688000 53360000 64032000 74704000 85376000 96048000 106720000 117392000 128064000 1387346000 149408000 160080000 GICA 011558 1 element 400 Chr 6 Human 400 CTCA 011558 3069941 000 VAMP V1 4 35 GTCA File Views Edit Tools Help VAMP is developped and registered by Institut Curie 0 10672000 21344000 32014000 42688000 53360000 64032000 74704000 85376000 96048000 106720000 117392000 128064000 138736000 149408000 160080000 GICA 011558
23. 617181 a7 ee LLEEEL LLLI LLL LL 3 4 35 6 7 amp 9 1011 12 13 14 15 1617181 xk Y ud 2X Y Wi xv pa 22X Y qi EY 122 X Y 6 7 amp 9 10 11 12 13 141516171819 22 X Y Human Figure 3 1 Typical VAMP window 3 1 1 Top left frame The top left frame is composed of several tabs controlling zooming search and drawing options see Figure 2 2 These functionalities are described in details in subsections 3 2 3 and 2 2 4 13 Ta Ld Search Arrays Search Elements Color Legend Figure 3 2 Top left Frame Zooming tab is selected 3 1 2 Bottom left frame The bottom left frame offers the choice between textual information on the object under the mouse pointer or context information called MiniMap figure 2 3 The information panel allows to retrieve array level information e g project id patient id or clone level information e g ratio chromosome position The MiniMap panel allows the user to easily visualize any clone name and its chromosome location Right clicking on one of the cytogenetic banding allows to open a contextual menu linking to public databases This menu can be configured as described in section 2 2 3 CGH Chromosome Merge es EE Da DE EE Chr Clone Count Date Genamicinstabilityl ype Hame NbRep NbSpot HumHista Organism Project Projectid Ratio Scale Team Clone Array Position Ratio Smt Weight 2796 Thu Apr 7 16 44 33 2005 CIN Cancers
24. 9 Search Arrays Panel The first array matching the search criterion is highlighted in the main frame see Fig ure 3 20 ODO VAMP V1 4 12 Point View File Views Edit Tools Help VAMP is developped and UU RE poeg e EB registered by Institut Curie 1 2 3 4 5 6 7 8 9101112131234 189802X Y Human A Cancer13 3 113r KRIS 44 Human A_Cancerl4 3 Point View 8 elements f CGH Chromosome Merge Chr 1 2 3 4 5 6 7 8 9 10 11 Clone Count 3104 Date Thu Nov 9 21 35 28 2 GenomicinstabilityType CIN ImgSoftware NA Name A Cancer17 3 NumHisto Cancer17 Organism Human NES T 1 eent p 5 T eh F e Dm pm 5 Ka ENS TS NT vars sat het EE te beak tte 1 2 3 4 5 6 7 8 9101112314 88418902X Y Human A nstitutCurie Figure 3 20 Search Arrays Panel and array highlighted in the main frame 24 The user can search for elements or objects this refers to the probes on the array e g clones matching his criterion such as Name RP11 140M23 see Figure 3 21 000 File Views Edit Tools Help RP11 140M23 Figure 3 21 Search Elements Panel The first clone matching the search criterion is highlighted in the main frame It is possible to simply pass from the first clone found to the following Three check buttons control the search output Pin up info Edit properties Put landmark see Figure 3 22 000 VAMP V1 4 12 Point View File Views Edit Tools Help VAMP
25. CLUIE AUL CXALMIPIC Ol SUGH all HILDOLU LIC 15 SIVOLL HI LIE ZIL Aa WEC IO Array files An Array file typically contains clone or probe level information for one or more chromosome of one or more samples It consists of an ArraySet in which one ore more Array elements are embedded Each of these Array elements regroups Obj elements which store probe level information for one particular sample The corresponding XML files has the following hierarchical structure lt xml vefsion 1 0 encoding 180 5959 1 15 lt ArraySet gt lt SetName gt Name lt SetName gt lt Array gt Array Properties lt Obj gt Obj Properties 0bj lt Obj gt Obj Properties 0bj Array Array Array Properties lt Obj gt Obj Properties 0bj lt Obj gt Obj Properties 0bj Array lt ArraySet gt We provide a short description of Array and Obj properties Array properties The following tags are mandatory lt Organism gt species lt Project gt project name lt Name gt array name ADNOUCIALCaG WILL tlle LOMOW IIS types Vull 15 LUM ONF alit VAtr do UESCLIOCA lll LAVIC Ratio the type of the signal value ratio M or log ratio L Url the physical localization of the XML files which contains the array data for each chromo some tag lt Chr gt these Urls are used by the software for saving analysis save command of File menu and restore any saved analysis loa
26. ChIP Probe Table 2 1 Default object types in the different types of arrays LOLY OO OLUCIS dle LOQuiread tO Use oO OL LUC VALVE LULICLIOL 5 LHe list OI Hiatal y OL required object tags depends on the array type In the two following paragraphs we describe the mandatory and optional tags we used for the two most widely used data array CGH data and transcriptome array data 10 lt X gt genome position integer lt Y gt ratio or log2 ratio value real consistently with the value of the array level tag lt Ratio gt M for ratio or L for log2 ratio lt Chr gt chromosome name 1 2 X Y lt Name gt clone name e g RP11 84M16 The remaining tags are not mandatory but they are required to activate some of the VAMP functions related to DNA copy number analysis e functions related to DNA copy number analysis lt Smt gt smoothing value smoothed value of signal for a Clone lt Bkp gt breakpoint a DNA breakpoint has been detected after this clone Out outlier clone with signal significantly different from its neighbors values are either 1 or 1 lt Gn1 gt clone status amplicon gain normal loss and double loss values are 10 for double loss 1 for loss 0 for normal 1 for gain 2 for amplicon These values may be calculated for example with the GLAD algorithm Hup et all The clone size tag lt Size gt value in bp is required for X zooming in up to the clone scale not a
27. Human gene profile holding the control key click on any other array CGH profile in the Tools menu click on Tools Genome Annotation Gene Selection see Figure 4 8 b A dialog box appear and set the parameters as follows see Figure 4 8 c la 2 for the From parameter select Region for the Results parameter select HTML report and save your file in gene list Now you can open a new web browser window and open the HTML file gene list html to visualize all the genes located in the amplified regions see Figure 4 9 59 CGH Affy SNPs gt ranscriptome P LOH ChIP chip b n VAMP Import Data r ber rrr CI VAMP Data Clustering o C CGH ARRAYS y Breakpoint Frequency e CI REPLICATION TIMING Cytogenetic Banding gt ZZ GENOME ANNOTATIONS Diffential Analysis P CH Human FrAGI Cl Arrays Genome Alteration Signal Histogram C Human Gene 3 Human Genomicvariant 3 Human_miRNA Genome Annotation Sample Annotations P Search Color Legend Y e 7 Chromosomes o C Mouse Chromosome Switch MP is developped and stered by Institut Curie A 3541 L2 12 0 6 0 6 0 0 0 0 0 6 0 6 1 2 1 2 1 8 1 8 2 4 2 4 3 0 3 0 Human Gene Selection Split Chromosomes Merge Chromosomes Filter A 3621 SH Sort by b 12 12 Import data Cancel Refres
28. LD 7 lt AxisKaryoSmallDisplayerFont gt lt AxisLabelFG gt BLACK lt AxisLabelFG gt lt AxisLineFG gt LIGHT_GRAY lt AxisLineFG gt lt AxisNorthSize gt 45 lt AxisNorthSize gt lt AxisSouthSize gt 40 lt AxisSouthSize gt lt AxisTranscriptomeFG gt GRAY lt AxisTranscriptomeFG gt lt AxisTranscriptomeLabelFG gt GRAY lt AxisTranscriptomeLabelFG gt lt AxisTranscriptomeLineFG gt BLUE lt AxisTranscriptomeLineFG gt lt AxisTranscriptomeReferenceFG gt 770033 lt AxisTranscriptomeReferenceFG gt lt AxisTranscriptomeReferenceLabelFG gt 770033 lt AxisTranscriptomeRef erenceLabelFG gt 3 lt AxisTranscriptomeRelativeLabelFG gt GRAY lt AxisTranscriptomeRelativeLabelFG gt lt AxisWestSize gt 90 lt AxisWestSize gt lt AxisXDisplayerFont gt Serif PLAIN 9 lt AxisXDisplayerFont gt lt AxisYCanvasPropertyNameFG gt BLACK lt AxisYCanvasPropert yNameFG gt lt AxisYDisplayerFont gt Serif PLAIN 9 lt AxisYDisplayerFont gt lt AxisYNameDisplayerFont gt Serif PLAIN 9 lt AxisYNameDisplayerFont gt lt AxisYPropertyNameFG gt BLUE lt AxisYPropertyNameFG gt lt BreakpointDashPadding gt 2 lt BreakpointDashPadding gt lt BreakpointDashWidth gt 2 lt BreakpointDashWidth gt lt BreakpointFG gt RED lt BreakpointFG gt lt SeachPanelBG gt 0RANGE lt SeachPanelBG gt lt SearchPanelButtonBG gt WHITE lt SearchPanelButtonBG gt lt SearchPanelButtonFont gt SansSerif PLAIN 9 lt SearchPanelButtonFont gt lt SmoothingLineFG gt BLACK lt Smoo
29. MenuItem type menu title External Links gt lt Menultem type url title NCBI Cancer Chromosomes url http www ncbi nlm nih gov entrez query fcgi db cancerchromosomeskamp term 2B Chr Arm Name amp amp cmd Search target blank lt MenuItem gt lt PropertyElementMenu gt lt UserDocumentation url gt indicates the physical localization of the user s guide several examples of how to call a cgi does not function locally lt Parameter key eXcel URL value http bioinfo curie fr cgi bin cghaia export pl format x1 gt lt Parameter key eXcelChrAvg URL value http bioinfo curie fr cgi bin cghaia average chr pl format x1l lt Parameter key cluster URL value http bioinfo curie fr cgi bin cghaia vamp_plugin pl action clust gt root of the physical localization of the data xml files lt Parameter key importData baseURL value file C VAMP data xml cgh gt indicates the physical localization of the image file which are used by the applet lt Parameter key applet_home_img URL value file C VAMP images applet_home png gt lt Parameter key cytoband URL value file C VAMP data xml cytoband human gt lt GraphElementIcon type CGH Array url file C VAMP images vamp cgh jpg gt lt GraphElementIcon type CGH Chromosome Merge url file C VAMP images vamp cgh jpg gt lt GraphElementIcon type CGH Array Merge url file C VAMP images vamp
30. Note that some movies present the main functions of VAMP for basic functions data Analy sis synteny analysis they are available at the following URL http bioinfo curie fr vamp doc An HTML v version of this manual with full size images also available at The manual is organized as follows e Chapter 2 describes the installation and the administration of the software e Chapter 3 presents the functionnalities of the software e Chapters 4 and 5 present two detailed analyses on real datasets Chapter 2 Administration manual 2 1 System requirements VAMP is a Java applet and therefore the Java Runtime Environment JRE must be installed on your computer before running VAMP We recommend to use Java 1 5 0 for better rendering and performances see http java sun com j2se 1 5 0 for download To visualize a large number of profiles simultaneously the java parameters regarding memory allocation must be correctly set For example if your computer disposes of 1 Gb of RAM memory the java virtual machine memory can be set with the following parameters Java virtual machine parameter setting Xms400000000 Xmx800000000 If you have more or less memory these parameters must be adjusted accordingly 512 Mb of memory is considered as a minimum and we strongly recommend to dispose of 1Gb Xms defines the minimal memory size allocated to the java virtual machine and Xmx defines the maximal memory size note that the X
31. Smt gt lt Bkp gt NA lt Bkp gt lt Out gt NA lt Out gt lt Gn1 gt NA lt Gn1 gt lt Properties gt lt 0bj gt lt Obj gt lt Properties gt lt Type gt Clone lt Type gt lt Y gt 0 009421 lt Y gt lt X gt 468000 lt X gt lt Chr gt 1 lt Chr gt lt Name gt RP11 82d16 lt Name gt lt Smt gt 0 0193950 lt Smt gt lt Bkp gt 0 lt Bkp gt lt Out gt 0 lt Out gt lt Gn1 gt 0 lt Gn1 gt lt Properties gt lt 0bj gt lt Obj gt lt Properties gt lt Type gt Clone lt Type gt lt Y gt 0 021783 lt Y gt lt X gt 2241000 lt X gt lt Chr gt 1 lt Chr gt lt Name gt RP11 62m23 lt Name gt lt Smt gt 0 0193950 lt Smt gt lt Bkp gt 0 lt Bkp gt lt Out gt 0 lt Out gt lt Gn1 gt 0 lt Gn1 gt lt Properties gt lt 0bj gt lt Array gt lt ArraySet gt 8 5 Transcriptome array XML file lt xml version 1 0 encoding iso 8859 1 gt lt ArraySet gt lt SetName gt chr1 lt SetName gt lt Array gt lt Organism gt Human lt Organism gt lt Project gt pollack lt Project gt lt ProjectId gt pollack lt ProjectId gt lt NumHisto gt NORWAY_7 lt NumHisto gt lt Chr gt 1 lt Chr gt lt Name gt NORWAY_7_EXPR lt Name gt lt Date gt 28 04 2004 lt Date gt lt Type gt TRS lt Type gt lt Url gt trs pollack NORWAY_7 a11 chr1 NORWAY_7_EXPR xm1 lt Url gt lt Obj gt lt Properties gt lt Type gt ProbeSet lt Type gt lt ObjectId gt IMAGE 322807 lt 0bjectId gt lt Signal gt
32. VAMP Administration and User Manual Version 1 4 39 June 18 2008 Visualization and Analysis of CGH arrays transcriptome and other Molecular Profiles Institut Curie Bioinformatics Unit D institutCurie Together let s beat cancer Contents 1 Introductio 2 Administration manua 2 1 System requirementg 22 Installation and configuratio 2 22 How to launch VAMP Ta onfieuratio 2 2 4 Data forma pee ne eee yeas BEER e CES _ e KEE Ss Search J sss e B eee e EE au 2 21 Installation 32 FrAGL Frequency of Amplicon Gain and Loss view 3 3 Finding common alterations among a collection of H array profiles KS lusterine profileg BEEN 36 onfrontation with sample annotation 3 Svntenv analvsid 8 onfrontation with Genome Annotation oe 310 Differential Analvsig 3 11 Correlation Analysig 4 Analysis example Bladder Cance 41 Introduction 2 4 2 Import the genomic profiles 4 Minimal Alteration computatio 4 3 2 isualization of the regions 43 1 Parameters settingd ALIOLOALC S CLIC 4 4 enome Transcriptome compariso KS omparison of the frequency between the two datasets 6 Availability 63 63 63 64 64 65 68 69 Chapter 1 Introduction VAMP is a graphical user interface for the Visualization
33. View gt Simple View h Point View Current View gt Double View gt Barplot View Specialized View gt Curve View g List View TATU EEE FPE ERES DOTE DotPlot View Karyotype Classic View Lea Figure 5 3 View menu New view 5 3 Frequency alteration computation 5 3 1 Computation for each dataset For each dataset compute the frequency of alterations by clicking on Tools FrAGL Compute see Figure 5 4 a Then set the Fr AGL parameters as follows see Figure 5 4 b 1 click on Status the alteration calling identified by the GLAD algorithm Hup et al 2004 is used 2 for the Minimum value of confidence click on Percent and set the value to 20 probe with a missing value percentage greater than 20 are discarded from the analysis Once this procedure has been performed for both 2004 and two new windows are displayed with the frequency of alteration see Figure 5 5 64 D File Views Edit CGH gt MP is developped and Affy SNPs tered by Institut Curie Transcriptome LOH ChIP chip Breakpoint Frequency gt Cytogenetic Banding gt Diffential Analysis b Genome Alteration D RELLEN GE Signal Histogram Chromosome Switch gt Genome Annotation gt Sample Annotations gt Color mE Filter Sort by D Misc D UE SA LSSESS SUES a Tools menu AGL b FrAGL parameters Figure 5 4 Frequency of alterations computation 5 3 2 Comparison o
34. X VAMP is developp Current View gt Point View Barplot View y Curve View Dee 2 listView 000000000 DotPlot View Show Breakpoints Show Smoothing Points Show Smoothing Lines Show Centromere Show Outliers Hide Size Show All Hide All Point Vi Hinhtlinht Minimal Alteratinn lt Figure 4 3 View menu Gained Lost Color Codes 4 3 Minimal Alteration computation 4 3 1 Parameters settings The minimal alterations or minimal regions of amplification correspond to the intersection for all tumors of the amplified regions These regions are minimal in that no breakpoint evidence is available to narrow the region further To compute the minimal amplified regions click on Tools Genome Alteration Compute see Figure 4 4 Then set the Genome Alteration parameters as follows see Figure 4 5 1 for the Minimum support of alterations click on Percent and set the value to 5 we want that the alteration is present at least in 5 of the samples 56 SS DN har SA 8E 00 SIDES Affy SNPs y stered by Institut Curi Transcriptome LOH ChIP chip Clustering Breakpoint Frequency Cytogenetic Banding Diffential Analysis FrAGL Signal Histogram Genome Annotation gt Sample Annotations gt L ul Color Legend V Chromosome Switch gt E Filter GH 18 Sort by 24 Misc gt LTE Figure 4 4 Tools menu Genome Alteration 2 for the Type of al
35. X Y Figure 3 28 File Print Standard Report Template 28 Use Z1JLCI SWELCILENLG LO ok HOUEC Dy CHCKITIS Oll LIE CALU VULLOIT YOU Call OCL OL IELUOVO several types of objects such as text molecular profiles images These objects can be dragged and dropped inside the template see Figure 3 29 KR SS VAMP Print Previewer File Edit Contents Templates Grid douglas public Point View a 6 7 H 9 10 11 12 1314 15 16171H PTE2 X Y 9 10 11 12 1315 1515171 KO ASA felt i amp 7 H 9 1 11 12 1314 15 16171HPTE2 X Y 5 7 H 9 10 11 12 13 14 I5 TG T EE X Y Oct 14 2005 1 1 Figure 3 29 Customized template minimap has been added to the standard template The menu File Print Print preview loads the last used template 29 The session can be saved in XML files Reloading the file later on allows the continuation of the analysis within the context of the previous work or the exchange of results and data with colleagues see Figures and 3 31 eee VAMPV14 BOB VAMP V1 4 SICH Views Edit Tools Help File Views Edit Tools Help M P Save View d Current View VAMP is developped and Save View M MAMER developped and Load View EE EE Load View gt in New View EE seu Gare Export Export replace in Current View import A Cancerl03 Import add in Current View A Cancers Update i M Update Configuration Se Con
36. ZoomPanelLabelFont gt SansSerif PLAIN 9 lt ZoomPanelLabelFont gt lt ZoomPanelTextFieldFont gt SansSerif PLAIN 10 lt ZoomPanelTextFieldFont gt lt PropertyAnnotations gt lt PropertyAnnotations gt lt CGHConfig gt 8 3 Import XML file lt xml version 1 0 encoding iso 8859 1 7 lt FolderSet gt lt Folder label CGH ARRAYS Team public gt lt Folder label snijders gt lt Folder label Arrays type CHR_ARRAY gt lt Item label gm00143 url public snijders array gm00143 xm1 gt lt Item label gm01524 url public snijders array gm01524 xm1 gt lt Item label gm13031 url public snijders array gm13031 xm1 gt lt Item label gm13330 url public snijders array gm13330 xm1 gt lt Folder gt lt Folder label Chromosomes gt lt Folder label chr01 type CHR gt lt Item label A11 arrays url public snijders chr chr01 xml gt lt Item label gm00143 url public all chr01 gm00143 xm1 gt lt Item label gm01524 url public al1 chr01 gm01524 xm1 gt lt Item label gm13031 url public al1 chr01 gm13031 xm1 gt lt Item label gm13330 url public al1 chr01 gm13330 xm1 gt lt Folder gt lt Folder label chr02 type CHR gt lt Item label All arrays url public snijders chr chr02 xm1 lt Item label gm00143 url public all chr02 gm00143 xml lt Item label gm01524 url public all chr02 gm01524 xml lt Item label gm13031 url public all chr02 gm13
37. add an hypertext link lt PropertyElementMenu object DataElement type Clone gt lt Menultem type separator gt lt MenuItem type menu title External Links gt lt Menultem type url title NCBI Clone Viewer url http www ncbi nlm nih gov genome clone clname cgi stype Namexamp list Name target _blank gt lt Menultem type url title NCBI Map Viewer url http www ncbi nlm nih gov mapview maps cgi 0RG humkamp query Name kamp MAPS cntg r clone sts genes comp amp amp CHR Chr kamp ABS_ZOOM 6M target _blank gt lt Menultem type url title Working Draft UCSC url data target blank token http www genome ucsc edu cgi bin hgTracks position chritChrH lt token gt lt sub gt lt property gt Position lt property gt lt token gt 150000 lt token gt lt sub gt lt token gt lt token gt lt add gt lt property gt Position lt property gt lt token gt 150000 lt token gt lt add gt lt Menultem gt lt Menultem type url title Ensembl ContigView url data target _blank gt lt token gt http www ensembl org Homo_sapiens contigview chr Chr amp vc_start lt token gt lt sub gt lt property gt Position lt property gt lt token gt 150000 lt token gt lt sub gt lt token gt amp amp vc_end lt token gt lt add gt lt property gt Position lt property gt lt token gt 150000 lt
38. and Analysis of array CGH transcrip tome and other Molecular Profiles VAMP was primarily developed for visualization and analysis of tumor sample array CGH profiles Several types of visualization are proposed for example classical CGH karyotype view or the genome wide multi tumor comparison views are available and allow the user to easily compare different arrays Additional information concerning each clone or DNA region can be retrieved interactively from different public databases through ex ternal links VAMP allows the user to confront the display of different types of molecular profiles such as array CGH profiles transcriptome arrays SNP Single Nucleotide Polymorphism ar rays Loss of Heterozygosity results LOH and Chromatin ImmunoPrecipitation arrays ChIP chips Many functions for analyzing CGH or other data are provided within the interface including looking for recurrent regions of alterations confrontation of genome data with tran scriptome data or clinical information clustering synteny visualization VAMP consists of a graphical interface written in Java 1 4 2 The software retrieves information from XML files making it easy to install it in any laboratory o is EEN with public Y sets Snijders et al Douglas et al et al de Leeuw et al 2004 Nakao et all 2004 2002 as which can be duc ds used This document describes the s configuration and the main functions of VAMP os os o os
39. ayed in the main frame i Profile View ii Karyotype View iii Dot Plot View iv List View These views all allow simultaneous visualization of several profiles the only limitation is the memory size of the computer running VAMP or more precisely the memory allocated to the Java virtual machine see section 2 1 for example with an 800 Mb Java virtual machine memory 700 microarrays each with 3500 probes can be loaded simultaneously Whatever view is chosen the profiles can be represented in Genomic mode or Chromosome mode The Genomic mode simply depicts the profiles along all the concatenated chromosomes It is the most usual representation and allows comparison of profiles from different samples or comparison of different types of profiles from a given sample The Chromosome mode is similar to the Genomic mode except that it only displays one particular chromosome It is also possible to merge several chromosomes and to represent those chromosomes useful for the study Profile View The Profile View can display the profiles as points barplots or curves see Figures and 3 10 The Profile View can also display symbols for chromosome telomeres and centromeres and can show the results of CGH ratio statistical analysis e g breakpoints or smoothed signal values see section 3 2 2 VAMP V1 3 15 Point View PIS Rie Views Edit Tools Help Le SS o NN Current View Point View Barplot View Cu
40. cale L 4 Ill Info LE HiniHap Figure 3 13 Karyotype Classic View Right clicking on a clone chromosome or array pops up a contextual menu 20 The Dot Plot View see Figures and 9 15 does not consider the microarray probe positions on the genome but only their ranks VAMP V1 3 15 DotPlot View Alle File Views Edit Tools Help NewView gt SimpleView h Point View Current View k Double View k Barplot View ii Specialized View Curve View Karyotype Classic View Figure 3 14 Views Simple View DotPlot View It displays a collection of samples as a heat map see Figure 9 15 based on the level of signal for each clone or using the Gain Loss Color Code Figure 3 18 VAMP V1 3 15 DotPlot View Me File Views Edit Tools Help VAMP is developped and registered by 5 6 7 8 9 011121314X60713 20322724 Institut Curie A B q d O LP d al el A Nr s sh i mpm I3 815 1 LAE AT M C T p ngo Um a 133 T3 P FIT iii mu a i Erol ees ee ta Eu Eds Jk EH Lat cor be Mer VW Lied Kg ioc cerra ers ele cd mew rst ee ie Bal bai Uo FE Kid P i T IH 6p W i pr W LT l p If lf m Hi WII ki seed Laia aaja E 1 etal aE rh HHE es titel ARS Tee aan sanan la pi yal ais JAN L E sq a masti H Than EM md a Aen BT rs MV en gei ke l e BAD var gn ee DA AA LI Pe 55 A aye ee Sh ll ud nl i SS i ro Lan AS AA s ra Aa sd
41. d command of the File menu The following tags are optional but filling them allows one to identify the patient and therefore to link together profiles from the same patient e g array CGH and transcriptome data lt ProjectId gt identification of the project lt NumHisto gt histological number which corresponds to a unique patient ID The tag lt SampleAdditionalData gt links array files with additional data e g clinical data that are stored for a given sample in an XML file as described in section 2 2 4 Any other tag may be added in the lt Array gt description They will be listed in the Info Panel of the bottom left frame figureB 3 and will be taken into account by the Search Arrays function section 2 2 3 Object properties Object descriptions are encapsulated as follows lt Obj gt lt Properties gt lt Type gt Obj Type lt Type gt other Obj Properties lt Properties gt 0bj lag Type describes the object type Any type description may be used but the default VAMP functions are associated to the following types Clone Probeset Microsat SNP and Probe There is default type for the objects of an array which depends on the array type as summarized in Table 2 1 Data type Array type Object type CGH array CGH Clone transcriptome arrays Trs Probeset Loss Of Heterozygosity data LOH Microsat Single Nucleotide Polymorphism arrays SNP SNP Chromatine ImmunoPrecipitation arrays
42. date of experiment and clone level information e g clone name ratio value chromosome number location The Array files are organized according to the follow ing hierarchy team projects Array files Each team may contain several projects and each project may contain several array files e the Import file which contains the list of projects and arrays that can be loaded within the VAMP as described in section 3 2 T VAMP distribution provides two scripts that generate these XML files automatically as described in section 2 2 4 vampTxt2xml generates Array XML files from CSV comma separated values files Files are available from the Download vampTxt2xml http bioinfo out curie fr vamp doc script vamp_txt2xml Array XML files http bioinfo out curie fr vamp doc data xml douglas Cancer3 xml CSV files http bioinfo out curie fr vamp doc data txt douglas Cancer3 csv The xml data file need to be copied into the root directory defined in the tag Parameter key importData baseURL value file yourRootDirectory gt as de scribed in configuration file syscfg xml section 2 2 3 GOILCCUOI y Files are available from the Download vampProject2import http bioinfo out curie fr vamp doc script vampProject2import Import XML file http bioinfo out curie fr vamp doc data import_data_public_xml public xml In case you need to generate your Array file
43. ding several profiles in the top panel 48 000 Views Edit Tools Help Save View F Load View h Export k 4 in Top Panel Update in Bottom Panel Configuration P Print h Close ha VAMP V1 4 12 Point View umati Cancer 3 A Larn 1 z rrs s d VAMP is developped and registered by Institut Curie pe crt rer ole ard ed er eb A hi 12 Sek bata X 4 5 j Figure 3 63 File Import in Bottom Panel Then the user must loading several pro files in the bottom panel eee File Views Edit CLES Help Top Panel Bottorn Panel CGH LOH VAMP V1 4 12 Point View Affy SNPs Transcriptome ChIP chip Clustering Breakpoint Frequency Cytogenetic Banding Diffential Analysis FrAGL Filter Sort by Misc Polnt View Figure 3 64 Tools Top Panel Differential Genome Alteration Signal Histogram Genome Annotation Sample Annotations Chromosome Switch da k 3 a 5 amp 7 8 91011121314 k i 9 AAA Compute 3 a 9 10111213141 k Redisplay sA k Reports TANE Sd ere HR MEIN 7 3 9101112131 K Merge Chromosomes 95m Split Chromosomes Ei ug p E T 2 3 ES 6 7 910111213141 1 2 Analysis Compute open a new window of dialog for Differential Analysis AQ 3 4 5 78 910111213141 The user can Test Statistical test is perf
44. e CGH ARRAYS blaveri 2005 Chromosomes chr06 directory see Figure 4 1 c Cd VAMP Data VAMP Data File Views Edit Tools Help E CGH ARRAYS Ef CGH ARRAYS E CH blaveri 2005 CH blaveri 2005 Save View ci Arrays gt 5 Arrays Load View LY 102 1 3 Chromosomes e E chro1 YA 106 1 DYA 119 1 e 3 chro2 Import 14 132 1 ES sh Update 5 ons e C chros Configuration gt n Ei chros x C Ait arrays Print DYA 162 1 34 103 1 14 179 1 El 106 1 DS a aaa a Da uid Import data Cancel Refresh Import data Cancel Refresh A RE a File menu Import b Genome wide profile im c Chromosome profile im port port Figure 4 1 Import Data The genomic protiles are displayed in the interface as shown in Figure 313 BREA NOS Saw RISO SENS See ig IN Eed UNIDA pa AS TASES al to PISO ps tom I B E 2 GE Ge Sr OWN SOT Patria DO ADAN EE e N SER ISO uj institutCurie Figure 4 2 Array CGH profiles Once all the data have been imported you can display the Gained Lost Color Codes see Figure 4 3 which corresponds to the alteration calling identified by the GLAD algorithm 2004 loss regions are in green normal regions in yellow gain regions in red and amplified regions in blue File Views Edit Tools Help New View X
45. ed Probe Status The Probe statuses i e the results of a segmentation algorithm of the whole genomic profile are used Regions Status hegions either selected manually or identified by our algorithm see sec tion 3 3 3 are used Exclude sexual chromosomes Different options are available Distance metric Euclidian Pearson and Manhattan distance are available Group metric Ward Single linkage Group Average and Complete linkage are available VAMP displays the results as a cluster view including a heat map and the trees resulting from the clustering algorithm Figure 9 45 39 606 Clustering Options VAMP V1 3 0 Dendrogram View VAMP is developped Hig pa Ss EWS We D O19 039 058 078 097 117 136 and registered by 123 4 56 7 8 9 10 11 12131415161719200 33 Institut Curie Li Dendrogram View 47 47 elements Annotation Legend ClinicalData B esos stable BB pets unstable Location Left B Location Right B Stage 1 H Stage 2 Stage 3 F mmm Ad EES M ER E Se pm _ 2 0 D 1415151719 0000 AAA 9 9 HH HH AE 332 D 019 039 058 078 097 117 136 23 4 56 7 8 9 10 11 Riasisienmanaz 43 tl a li 4 js Figure 3 45 VAMP interface Dotplot view of array CGH profiles middle panel and dendrogram resulting from a hierarchical clustering right panel In between color coded clinical information about the samp
46. ed by Institut Curie i D b xn Transcriptome b LOH gt ChiP chip A_1333 4 14 Clustering Breakpoint Frequency Cytogenetic Banding Diffential Analysis FrAGL Genome Alteration Signal Histogram Genome Annotation Sample Annotations Chromosome Switch Filter i Sort by _ Misc Figure 3 48 Tools Sample Annotations Clinical property The user opens a dialog box where he can easily choose the available clinical properties VAMP Sample Annotation Panel _ Hide Annotations OK Apply Remove Cancel Figure 3 49 Sample annotations The user chooses clinical properties to be visualized This data can be visualized as color coded bars in an annotation frame on the left of the profiles and can be easily compared with a clustering result Figure 8 50 42 Dendrogram View 47 47 elements Annotation Legend ClinicalData B esce stable F ics unstable D Location Left l Location Right Stage 4 B stage 2 Bg stage 3 E Stage A Figure 3 50 VAMP interface Dotplot view of array CGH profiles middle panel and dendrogram resulting from a hierarchical clustering right panel In between color coded clinical information about the samples with a legend botto
47. element Figure 3 51 Switch or Add The user can replace a profile by its projection onto another species genome by using Synteny Switch or he can add the projection below the original profile in the same window by using Synteny Add In order to see the links of the syntenic projection perform as described in Figures 3 53 and 45 Unaverage Transcriptome VE C UU S 8 8 9 10 11 13 12 44 15 16 LOH Change CGH Ratio M to L ChIP chip Change CGH Ratio L to M d Affy SNPs Split Chromosomes Genome Annotation Merge Chromosomes Chromosome Switch Minimal Alterations Sort by Recurrent Alterations Filter Sample Annotations Clustering Synteny Switch Add Synteny i 08 Misc coming Search Arrays Search Elements Color Legend i Y Range Point View 1 element Figure 3 52 Add Region Synteny The user can projects only those clones that are comprised in the regions he has defined by using Synteny Add Region Synteny Results are shown in the next figure VAMP V1 3 15 Point View Edit Tools Help EX se Slat UE Te a Point View ia G A 2 UQ o n MUD 80415 a6 EE Barpiot View Y Curve View ST List View Hits sb xs A gt liiw EE Ale ak DotPlot View ef er m PS W db E tr pia GainediLost Color Codes 08 1 d o Ki Ll Show Breakpoints Show Smoothing Points Show Smoothing Lines 04 Show Centromere 03 Booming Show Outli
48. erations Choose Minimal regions At least 50 of the profiles must share the same alterations 39 br r Carneerls 1 2 0 3 0 6 03 m 0 0 o 8 0 3 0 6 0 9 2244000 44568000 br rCapcer b 1 2 0 9 LE 0 8 EEL n 41 E 0 34 0 8 3 22484000 44368000 rs Career 1 2 0 3 0 6 0 3 0 0 0 3 6 0 3 22424000 44965000 hr Cancerl 1 2 0 3 DE 3 m S 0 0 0 3 0 6 0 9 edit 6000 ars Careers 1 2 0 3 0 6 03 0 0 E 0 3 0 6 0 9 2244000 44968000 Figure 3 39 Minimal Alterations Results Nou E eg a O S000 239986000 112420000 134304000 157398000 2000 839936000 112420000 124304000 157398000 gain green for loss Here there is only one loss region 36 m P 4 a 5 rU E n we the minimal alterations are drawn in red for Engen A iJ fe File Views Edit REHA Help VAMP is developped and registered by Institut Curie Transcriptome LOH ChiP chip Clustering Breakpoint Frequency Cytogenetic Banding gt mi Diffential Analysis fe ra oO Genome Alteration Signal Histogram Genome Annotation Sample Annotations Chromosome Switch Filter Sort by Misc Figure 3 40 Tools Genome Alteration Compute The user opens a new dialog window to set the parameters for Recurrent Alterations 000 Genome Alteration Dialog Figure 3 41 Recurren
49. ers pa MAPS 01 Search El Hide Size Color Legend Y Ra 00 Show All 2 3 q AL 1151205 GR gt 15016 3 PE Point Hide All ip 183 2 elen 12 Hightlight Minimal Alterations m Chr 1 Mouj Hightlight Recurrent Alterations n MAPL 15F Show Annotations 09 3 att I 08 q a qa 07 ob m ae Figure 3 53 Show Synteny Links The user can visualize the links of synteny using Current View Show Synteny Links Results are shown in the next figure VAMP V1 3 15 Point View File Views Edit Tools Help VAMP is developped and registered by Institut Curie MPLT 14GN2 477 24 MPLT_14GD2 477 24 21 12 Chr2 Mouse 400 MPLT_14GM2 477 SEI 12 A ht JI i ll LUI H Sa 59 0 Cip 539 B o4 15 16 17 181920222 X Y 6 8 9 10 11 12 13 M 15 16 17 1819 X Y Z Mane institutCurie Figure 3 54 Synteny visualization A complete example of visualization of synteny The original mouse profile is on the top its projection onto the human genome at the bottom and the projection of the clones from the two highlighted regions in the middle with links from the mouse ordered profile to the human projection 44 With VAMP it is possible to compare a molecular profile with genome annotations for example gene structure the user can load a pseudo profile with the structure of all known genes introns exons splicing variants Several functions are offered Proceed as follows e import the
50. es Show Hide Breakpoints Show Hide Smoothing Points Show Hide Smoothing Lines Show Hide Centromere Show Hide Outliers Show Hide Size Show All Point v Hide All 31 ele Hightlight Minimal Alterations Cancer Cancer 10 Cancer 11 Lancer 1z Lancer 13 Lancer 15 Cancer A0 Cancerz1 Cancers Cancers Cancerzd Cancer A Lancerzb Cancerz Cancerza Cancerz3 Cancers Cancer 20 Cancers Cancers Cancers3 Cancers Cancers5 Cancer 26 Cancers Hightlight Recurrent Alterations Cancerd Cancers Show Annotations Gees Cancer Show Hide Synteny Links Cancers Cancer3 Show Hide Tags Show Hide Tag Strings LM ShowiHide Info ange minata Show Hide Out of bounds Info Figure 3 16 Views Current View List View Display additional features Additional features regarding array CGH profiles can be displayed within VAMP provided that these features are available in the Array XML files see 2 2 4 For example the profiles Hup et al could have been preprocessed by any segmentation algorithm like GLAD ell 2 the following additional features are available within the menu View Current View see Figure 3 17 and 8 18 Gain Loss Color Code each clone is colored according to its status loss in green normal in yellow gain in red and amplicon in blue Show Breakpoints a vertical red dashed line is plotted and represents the b
51. f array CGH data analysis see section 2 2 2 26 VAMP Is developped and i f n Ep O voy ge KAY Ys registered by Institut Curie 1 2 3 4 5 6 37 8 9 10 11 12 1314 1516171819822 X Y Human A Cancer10 3 12 04 an eC EET EPL UHT 12 35 Human 4 5 6 7 8 9 10 11 12 1314 1516171819092 X Y A_Cancer113 1 2 3 4 5 6 7 B 9 10 11 12 13 14 15161718199 2 X Y MAA Gain Color f Echantillons HSB RVB Restore Default Search Elements Color Legend EI 13 14 15 16171812 T2 X Y Le Point View 8 elements LLL 13 14 15 16171819 T2 X Y f a Chr 1 Human 400 400 899 A Cancer12 3 13 14 15 161718 2222 X Y RM 13 14 15 151718 Q PP2 X Y OORT 13 14 15 1617181 QIPP2 X Y LULU UL RRARANI il mI Apercu D O e Echantillon de texte Echantillon de texte mi O Echantillon de texte Echantillon de texte n t DS 4 amp FS TUTO c 7 9 10 11 12 1314 15 16171819 P2 X Y Human institutCurie Figure 3 25 Color Legend Panel X and Y scaling The user may change the vertical range either for one particular array Local option or for all arrays displayed Global option see Figure and 3 27 S2 VAMP V1 3 15 Point View File Views Edit Tools Help EISE Apply Restore Default Booming Search Lrrayz Search Elements Color Legend Figure 3 26 Y Range Panel In the
52. f the frequency between the two datasets To compare the two FrAGL profiles obtained in the previous step for each datasets proceed as follows 1 in the first FrAGL view select and copy the profile see Figure 5 6 a 2 in the second FrAGL view paste the profile see Figure 5 6 b The comparison in now possible in the final view as shown in Figure 65 D VAMP V1 4 12 FrAGL File Views Edit Tools Heip VAMP is developped and registered by Institut Curie 11 12 138 14 15 16 17 18 18 202122 X Y Human FrAGL 85 0 8 08 0 7 Zooming Search Arrays L Search Elements Color Legend Y Range FrAGL 1 element FrAGL Chromosome Merge Array Count 85 Chr Clone Count ImgSoftware Name FrAGL 85 Organism Human Project douglas 2 Projectld douglas 2004 Ratio alse Ratio Scale Support Team Clone Array Chr Confidence DataSource Frequency Gained Count Gained List 0 7 h Human 1 2 3 4 5 6 H 8 3 10 11 12 13 14 15 16 17 18 13202122 X Y 11 12 13 14 15 16 17 18 19202122 X Y Human Info MiniMap institutCurie Figure 5 5 Frequency of alterations the Douglas et al 2004 dataset E Undo VAMP is developp Redo registered by Insti Go before A File Views Edit Tools Help Undo Import 41 Profiles Redo Go be
53. figuration P Print V geg Print P Human Close A Cancer 3 d op D cl 2 Hirn A Cancer 24 12 daher nl mal Figure 3 30 Save and Load menus VAMP V1 3 15 Point View PIE File Views Edit Tools Help 6 T 8 8 101112321314151617199B12 OY Human 5 conf xmi 5 conf A0 vm 3 VW vm Conf 1 xml i confdemo xmi conf2 xml TN CONFHEW xml 5 conf 3 vm 5 dot vm Y cont4 mt TN philxml CONF5 xml phupe xml Y coNF 24 ml um Hom de fichier cancer12 Fichiers du type 05 sje L rest be gro S CMT el ll al Pelt orien fo date ib bu lipa Ale 1 nds cm 5 8 9 101112121401587189022x Y 6 T 8 8 1011121314151 7129022 E Y Human institutCurle Figure 3 31 Save dialog window There are three possibilities to load a saved session in New View replace in Current View or add in Current View 30 The VAMP software allows a large variety of analysis to be performed by the users Some of the tools provided are profile specific e g tools dedicated to array CGH or transcriptome data analysis Other generic tools can be used with any type of molecular profile You will find below a list of the main analysis tools available within VAMP 3 3 1 Manual analysis Among the numerous functions of VAMP the user has the possibility to put his own marks and regions This is done by right clicking on clone probe element under the mouse pointer of any mo
54. fore b d Copy E EN Cut Paste opy AMP egisti Lut Paste Unselect all profiles Remove all regions all landmarks Lock panel nn alamant Select and copy Rarantar a Edit menu Select and copy b Edit menu Paste Figure 5 6 Comparison of the two FrAGL profiles 66 A VAMP V1 4 11 FrAGL x File Views Edit Tools Help VAMP is developped and registered by Institut Curie 15 16 17 18 19 2021272 X Y Human FrAGL 85 0 8 0 7 0 6 0 5 0 4 f 0 3 T K i 1 2 3 4 5 6 7 8 3 10 Zooming Search Arrays Search Elements Color Legend Y Range FrAGL 2 elements ils FrAGL Chromosome Merge 0 7 Array Count 85 Human 16 17 18 19202122 X Chr 1 2 3 4 5 6 7 8 9 10 11 FrAGL 125 Clone Count 3104 08 ImgSoftware NA 0 7 Name FrAGL 85 05 I Organism Human 05 Project douglas_2004 04 Projectid douglas_2004 J Rad 03 Ratio False T 16 17 18 19202122 X Y Ratio Scale L UIW d 1 4 5 2 3 Support l Figure 5 7 Comparison of the frequency of alteration for 2004 top profile and bottom profile datasets Team CGH Clone Array FrAGL 85 Chr 2 Confidence 0 988 DataSource UCSC Frequency 0 190 Gained Count 16 15 16 17 18
55. genome annotation data see Figures e put a landmark on your favorite gene and center on it see Figures 3 56 8009 Load View 1 2 Sans titre17 Export Import Update Configuration gt Print gt Close P REPLICATION TIMING Y GENOME ANNOTATIONS Y Human Y Arrays Human_GenomicVariant Human_miRNA P Chromosomes Er Point View 1 element Gel Chr 1 Human 400 A Cancer1 3 VAMP is developped and registered by Institut Curie Figure 3 56 Genome Annotation Then you can put a landmark on your favorite gene and center on it 45 VAMP is developped and OOOO LEE A Cancer15 3 Figure 3 57 Genome Annotation zoom 3x Right clicking brings up a menu which allows to open web pages from NCBI gene UCSC Genome Browser or Ensembl ContigView see Figures 9 58 VAMP is developped and registered by Institut Curia a gm E SE aum CR E E l E a M SS 1 umm 1 Wi Gene AK126625 Center on Gene Pin up info Put landmark Put landmark and center Put begin landmark Put end landmark Edit properties Copy ID in search panel External Links 4 NCBI Entrez Gene NCBI Entrez Nucleotide Ensembl ContigView Figure 3 58 Genome Annotation zoom 30x exons in red introns in yellow UTR 3 in light green and UTR 5 in dark green 46 The Histogram of the signal can be computed over the profiles
56. h Misc b oe Y EE ERE Oe e se mmm os a Human gene import b Tools menu Genome Annotations Gene Selection Dialog Gene Selection Dialog Consider All genes O Only genes overlapping with probes O Only genes not overlapping with any probe From O Anywhere e Regions only Results 0 HTML report HTML report help O CSV report export CSV help Display Profile display profile help OK Cancel c Genome Annotations parameters Figure 4 8 Candidate gene retrieval Gene Selection Iceweasel Fichier Edition Affichage Historique Marque pages Outils Aide lt a z z t IS file home phupe doc publications CTuDB scenario gene list html sl b ine IS MP Getting Started E Latest Headlines MH D sactiver Cookies 5h C88 S Form z Images Information E Divers LZ Entourer 3Redimensionnere 2 Outils T Voir Source t Opti Consider All Genes E From Regions 5 1080500314 1080916946 1080917217 1082255506 1082105471 1082494439 1490707741 1499530341 1878525550 1881647840 EEE Ok k s Clone Gene Name Nmc Chr Position Size Ratio GeneSymbol Chr GeneBegin GeneEnd Size Strand NbExons mRNA_ID RP11 4384 nul B 20184238 352 RP11 159C08 null 6 20442776 179800 E2F3 6 20510376 20601920 91544 7 NM 001948 RPTI 158C8 nul 6 20442776 173800 E2F3
57. ic hybridization analysis of colorectal cancer cell lines and primary carcinomas Cancer Res 64 4817 4825 Gysin S Rickert P Kastury K and McMahon M 2005 Analysis of genomic DNA alterations and mRNA expression patterns in a panel of human pancreatic cancer cell lines Genes Chromosomes Cancer 44 31 51 Hup P Stransky N Thiery J P Radvanyi F and Barillot E 2004 Analysis of array CGH data from signal ratio to gain and loss of DNA regions Bioinformatics 20 3413 3422 Kaufman L and Rousseuw P 1990 Finding Groups in Data An Introduction to Cluster Analysis Wiley Series in Probability and Mathematical Sciences La Rosa P Viara E Hup P Pierron G Liva S Neal P Brito I Lair S Servant N Robine N Mani E Brennetot C Jannoueix Lerosey I Raynal V Gruel N Rouveirol C Stransky N Stern M H Delattre O Aurias A Radvanyi F and Barillot E 2006 VAMP Visualization and analysis of array cgh transcriptome and other molecular profiles Bioinformatics 22 2066 2073 Nakao K Mehta K R Fridlyand J Moore D H Jain A N Lafuente A Wiencke J W Terdiman J P and Waldman F M 2004 High resolution analysis of DNA copy number alterations in colorectal cancer by array based comparative genomic hybridization Carcinogenesis 25 1345 1357 Patil M A Gutgemann I Zhang J Ho C Cheung S T Ginzinger D Li R Dykema
58. idy A Spraggon C Graham A Southgate J Asselain B Allory Y Abbou C C Albertson D G Thiery J P Chopin D K Pinkel D and Radvanyi F 2006 Regional copy number independent deregulation of transcription in cancer Nat Genet 38 1386 1396 Veltman J A Fridlyand J Pejavar S Olshen A B Korkola J E DeVries S Carroll P Kuo W L Pinkel D Albertson D Cordon Cardo C Jain A N and Waldman F M 2003 Array based comparative genomic hybridization for genome wide screening of DNA copy number in bladder tumors Cancer Res 63 2872 2880 T1 Chapter 8 Annexes 8 1 Main configuration XML file lt Parameter key min memory value 200 gt minimum size for a standard use a message is displayed if the user memory is below this threshold lt Proxy host www cache port 1234 gt proxy address for the URL lt TranscriptomeURLTemplate gt file C VAMP data xml trs ProjectId NumHisto chr chr ChrAlias xml lt TranscriptomeURLTemplate gt Used for locating the transcriptome data from a CGH array variables are set from the XML CGH array data files lt LOHURLTemplate gt file C VAMP data xml microsat ProjectId NumHisto chr chr ChrAlias xml lt LOHURLTemplate gt Used for locating the LOH data from a CGH array variables are set from the XML CGH array data files Parameterization of the contextual menu of an object of Clone type how to
59. iles which is connected to Array CGH In the example below we compare array CGH top profile versus transcriptome ratio second profile in descending order computed for Affymetrix U95 array of a bladder tumor sample and of a reference sample This confrontation pinpoints the probable implication of the oncogene cyclin D1 in this tumor The third and fourth profiles in descending order correspond to a reference profile average normal bladder tissue profile and the profile of the tumor under study respectively The second profile is the ratio of the fourth to the reference profile VAMP V1 2 41 Point View File Views Edit Tools Help 2020 at 69150723 Figure 3 47 CGH vs Transcriptome An icon at the left of each profile shows the type of loaded profile 41 Clinical data or any other sample annotations present in the additional XML files see sec tion can be visualized in the interface or used for filtering tumors or for sorting them the link between additional data and molecular profile is based on the XML tag lt NumHisto gt representing a unique patient ID see section 2 2 4 To add any clinical properties in the current view just do the following e open the dialog to add clinical properties see Figures 3 48 e choose the properties you want to display see Figures 2 49 eoe VAMP V1 4 12 Point View File Views Edit Tools Help gt CGH PIAMP is developped and Affy SNPs pegister
60. is developped and registered by Institut Curie 3 4 5 6 7 8 9 10 11 12 1314 1516171812022 X Y Human r E EEN E EIERE Let E RAR el Point View 8 elements 23999999463558197 11999999731779099 4 5 6 7 8 9 10 11 12 1314 1516171812022 X Y Human Z isttuiCurie Figure 3 22 Search Elements Panel Zoom The user can zoom in or zoom out on molecular profiles zoom scale is logarithmic see Fig ure 3 23 Fit checkboxes force the horizontal and or vertical scale to fit the window size man VAMP V1 3 15 Point View File Views Edit Tools Help VAMP is developped and registered by Institut Curie Zooming Search Arrays b Point View 8 elements a Chr1 Human 400 pe Ts Cancer18 Figure 3 23 Zooming Panel Color codes By default points or barplots are colored according to the signal intensity generally using ratios of the two channels or log ratios using a continuous scale from red to yellow to green The user can easily change the thresholds and colors of the clone ratios either for one particular array Local option or for all arrays displayed Global option see Figure 3 24 and 8 25 AAA File Views Edit Tools Help v Restore Default _ Y Search Elements Color Legend Ab Figure 3 24 Color Legend Panel For each of the views described in section 3 2 2 molecular profiles can be colored according to the results o
61. lecular profile A menu appears as shown in Figure 8 32 allowing various actions to be performed VAMP is developped and registered by Institut Curie og 9 10 11 12 13 14 15 141718002 X Y Human AAA Clone RP11 445K1 A Cancer 1 3 13 Center on Clone Pin up info Put landmark Put landmark and center Put begin landmark Edit properties Copy ID in search panel NCBI Clone Viewer NCBI Map Viewer Working Draft UCSC Ensembl ContigView 7 8 9 10 11 12 13 1415 1681718 TE P2 X Y Human instit utCurie Figure 3 32 Contextual Menu The user can easily put landmarks and regions of biological interest Within the contextual menu it is possible Center on Clone Probe to center the profile around the current position Put landmark to draw a vertical bar trough all the profiles to define a locus Put begin landmark Put end landmark to draw a region over the set of profiles External links to retrieve any information from public or local databases It is possible to add your favorite database see section 2 2 3 The user can customize colors by right clicking onto landmarks and regions and then using Set colors for a better visualization see Figure 9 33 ol 12 Haman A Cancer1 3 Pin up info Sort CGH arrays 0 Center on region 0 M Remove region and landmarks d Ae More AS TALA Remove region but not landmarks ax vh rie Edit properties oa Set color 4 Default mE Light Green
62. les with a legend bottom left Data from 40 VAMP proposes several data manipulation procedures for the profiles such as loading any type of profile CGH expression LOH ChIP chip for a given sample A typical application of VAMP is the simultaneous visualization of the DNA alterations and gene under and over expression in a region see Figures 3 46 and 3 47 In the case of one color microarrays such as Affymetrix the user can define a reference profile and compute the ratio with a test profile he can easily compare the ratio of gene expression with the DNA alteration eoe VAMP V1 4 12 Point View File Views Edit Help GH Affy SNPs Transcriptome Load Related CGH Array AMP is developped and pegistered by Institut Curie 1 2 3 4 5 f 3 LOH ChIP chip Average Unaverage Clustering L Relative 9 NM 4 3 Y Breakpoint Frequency gt Absolute Cytogenetic Banding P Reference Array Diffential Analysis Split Chromosomes FrAGL P Merge Chromosomes 3 Te e 3 Genome Alteration Split Signal Histogram Merge Genome Annotation Correlation Analysis pannan Sample Annotations TEM i ae 3 Change Intensity to Logintensity si Chromosome Switch P Change Logintensity to Intensity FINE d ri irc NR A M D 1 Sort by Misc Haman 4 5 amp J 3 DESEE o A Figure 3 46 Transcriptome Load The user can load expression profiles The user can load and visualize one expression prof
63. m left Data from 3 3 7 Synteny analysis VAMP can display the syntenic projection of a profile onto the genome of another species which serves as a reference a typical application is the projection of a mouse array CGH profile onto the human genome Figure 3 54 In such a case the mouse clones are ordered according to their mapping onto the human genome VAMP uses pre computed information mapping each clone of the sample array onto the reference genome The synteny relationships can be shown for a selection of regions of the genome as links from each clone of the profile to the location of the most similar sequence of the reference genome To perform the syntenic projection over the whole genome or on genomic regions do as described in Figures and VAMP V1 3 15 Point View File Views Edit Tools Help CGH Average Unaverage 1 2 E 4 ei 6 7 e 9 1 11 12 D M 15 16 Change CGH Ratio M to L Change CGH Ratio L to M Transcriptome LOH ChIP chip Affy SNPs A aii Split Chromosomes c ahs How SH ee Frak Minimal Alterations RA dp Galen AT TET Recurrent Alterations lt Zana A 5 erat Ts Clustering sed ae EES Chromosome Switch Sort by Filter Sample Annotations Misc gt b D Genome Annotation gt Merge Chromosomes gt gt gt gt D Booming Search Arrays Search Elements 07 07 Color Legend Y Range Io Point View gs Ge 1
64. mbol in the drop down menu 2 type E2F3 in the right box 61 4 wait for the search to be completed it may take few seconds 5 zoom in in the X and Y scale see Figure 4 7 b until to see the E2F3 gene structure see Figure 4 11 c The E2F3 gene is located in the amplified region previously detected VAMP is developped and registered by Institut Curie ProbeSet 41632_AT Center on ProbeSet Pin up info Edit properties Copy ID in search panel Thu Sep 6 16 26 50 2007 GTCA 152644 Correlationld Human ioScale L b IL GTCA 162644 b Color Legend Y Range a External links Genecards b Search panel E2F3 c E2F3 gene structure Introns are in yellow exons in red and 3 UTR in green Figure 4 11 E2F3 is correlated with DNA copy number 62 Chapter 5 Analysis example Colon Cancer 5 1 Introduction This scenario presents the guidelines to compare the frequency of alterations obtained in two colorectal cancer datasets Douglas et all Rood Nakao et al To run the interface you need to configure your Java Virtual Machine as explained at http bioinfo curie fr actudb Java configuration html At least 1Gb RAM memory is necessary on your computer 5 2 Import the genomic profiles First start the VAMP software La Rosa et all 2006 from the web page http bioinfo curie fr actudb access php Then load the array CGH profiles as follows 1
65. mx can not exceed the size of the RAM memory In the example below the memory allocation ranges from 400Mo up to 800Mo With these parameters the users can load up to 700 microarrays each with 3500 probes simultaneously For more details please visit http bioinfo curie fr tutorial vamp Java configuration html 2 2 Installation and configuration 2 2 1 Installation VAMP can be installed either in standalone version or in intranet server version standalone version Windows once you have retrieved and extracted the VAMP tar gz file just copy the VAMP directory into the C directory If you want to install the software in a different directory you have to replace the default path C VAMP with the new path in the following configuration files cgh htm1 configuration xml syscfg xml and configuration xml print report xml standalone version Mac OS X Unix Linux once you have retrieved and extracted the VAMP tar gz file just copy the VAMP directory in any directory You have to replace the default path C VAMP with your new path in the following configuration files cgh html configuration xml syscfg xml configuration xml print report xml For exam ple if you have copied the VAMP directory into usr local you replace file C VAMP with file usr local VAMP COPY UE VALVE CHICCUOLYy HILO LIC LOOL ULECLOL y OL YOUL WCDSCL VEL 101 CAGIILDIC 111 LLO directory http hosted myHome com html of your apache server The follo
66. oice made within the Compute dialog p values significance level assigned to each correlation coefficient FWER p values adjusted for multiple comparison in order to control the Family Wise Error Rate FWER that is the probability that one or more loci among those selected is a false positive We use the Holm adjustment procedure which is more powerful that the traditional Bonferroni procedure FDR p values adjusted for multiple comparison in order to control the False Discovery Rate FDR that is the expected proportion of false positives among those loci selected These FWER or FDR multiple testing adjustments may be performed for the whole set of genes whole genome or for each chromosome separately by chromsome leading to a less conservative adjustment If only one chromosome is selected choosing whole genome or by chromosome therefore gives exactly the same results Importantly all adjusted and unadjusted p values are displayed in 10 log scale so that significant genes with small p values can be easily seen For example a gene with p value 1077 will be plotted with y 7 Also note that all p values are given the sign of the corresponding correlation coefficient which may be negative for some genes Exporting the results The results of the Correlation Analysis cannot be exported yet 09 1 element Clone Array GTCA_011558 Chr 6 CorrelCoef 0 888 Correlationld 416
67. ormed using either Student or Welch test Color bars Use sign If the probe mean of the group in the bottom panel is greater than the probe mean of the group in the top panel the bar is displayed in red and otherwise in ereen Color bars Use confidence Color bar corresponds to the percentage of profiles without missing values Max P Value Probes with a p value greater than this value are discarded Multiple testing Benjamini Hochberg ajusted p values using Benjamini Hochberg method Multiple testing Benjamini Yekutieli ajusted p values using Benjamini Yekutieli method Results The results are displayed in a profile view see Figure 3 66 The values correspond to log Op value Report The results are saved in HTML or CSV file P dm Te I 1 L Differential Analysis Parameteres Differential Analysis Parameteres Test tt aal Student e Colorbars f Use sign Kx a Use confidence Max P Value Multiple Testing None C Benjamini Hochberg Benjamini Yekutieli Results fei Display profile 2 HTML report C CSV report Figure 3 65 Differential Analysis dialog Different options are available 50 File VAMP is developped and A gt registered by Institut Curie 1 2 3 4 5 6 7 8 9 10 11 12 13 1415161718 0022 X Y Human ANADIFF 1145152 25 25 24 23 Differential Analysis 1 element Differential
68. reakpoint location Show Smoothing Line and Show Smoothing Points the piecewise constant function es timated by the segmentation algorithm is plotted Show Outliers outliers see page I for a definition of outliers are black circled 22 VAMP is developped Barplot View Curve View List View DotPlot View Gained Lost Color Codes Show Breakpoints Show Smoothing Points Show Smoothing Lines Show Centromere Show Outliers Hide Size In LS Show All es Hide All DA n3 Poi Hightlight Minimal Alterations g 04 3 ele T 02 Hightlight Recurrent Alterations VAMP is developped and registered by 15 16 17 18 19202122 X YY Human Institut Curie 1 2 3 4 5 6 8 9 10 11 i 13 i4 15 16 17 18 19202122 X Y Cancer 4 10 10 W I D 06 0 6 0 D 02 F 024 ax Em Oo HS 2 DES EF Op E HEI 8 150 el D Human 1 2 3 4 5 amp 7 8 9 10 11 12 13 14 15 16 17 18 19202122 X Y 5 7 l 2 3 a 5 5 T Ei 9 10 11 12 13 12 15 16 17 18 192001283 X Y x Y Hinman institutCurie Figure 3 18 Additional information with Gained Lost Color Codes Show Breakpoints Show Smoothing Lines and Show Outliers 29 A function is available to search for any array level of probe level information in the data Search for arrays The user can search for arrays matching his criterion such as Name Cancer11 see Fig ure 9 19 600 File Views Edit Tools Help Figure 3 1
69. rve View Figure 3 9 Views Current View Point View After importing the genomic profiles see section 8 2 1 it is possible to switch from one type of representation to another The main frame can be split into two frames see Figure D UU The upper frame can for example contain a profile for reference when browsing a collection of profiles in the lower frame The two frames have separate control of Y scale and Y scrolling but have the same X scale and X scrolling 18 File Views Edit Tools Help AMP iz developped and See by Search Arrays T Search Elements Color Legend l T Range Poirt view E elements Chr2 Human 400 Cancer 7 amp 9 10 11 12 13 1415161718128 22 X Y Human 5j ioni I ic im T aaki W 2 3 4 fe at uS Q 10 11 12 13 14 151617181 t E Y a cd Lo ted i 2 3 4 5 6 9 11 HB 14151617181 ZER ER a SL LL LTELLL ell Mj 2 3 4 5 Be S g amp 10 11 12 13 1415 161710140 X Y 09 S Lea erc VW d 3 S B 7 x l 11 12 13 14 15 1617181 22 E Y e SKI Le lo AD Se w Isi 3 3 4 5 6 7 8 9 1011 12 13 4151617121822 E Y S SIb LEE 5 6 7 oh 1011 1 1 14 15 1617181 BEY Figure 3 10 Profile View Point View NW E File Views Edit Tools Help New View Current View m Ao ma E 0 un n m am 0 0 Figure 3 11 Views New View Double View Point View The user can open a new double view see Figure
70. s without using these scripts subsection 2 2 4 provides a detailed description of corresponding XML tags Scripts for automated data generation Array files can be generated by the script vampTxt2xml As an input this script takes csv comma separated value text files The field names must correspond to the tags listed in section 2 2 4 and the file must be ordered by chromosome and position We give an example of such an input file below Y X Chr Name Smt Bkp Out Gnl Weight 1 658040e 01 3247817 1 RP4 785P20 0 020635750 0 0 0 NA 1 316050e 01 4487199 1 RP1 37J18 0 020635750 0 0 0 NA 9 597111e 02 58717818 1 RP11 49J3 0 020635750 0 0 0 NA 3 588748e 02 7071571 1 RP3 438L4 0 020635750 0 0 0 NA 1 012979e 01 7653186 1 RP11 338N10 0 020635750 0 0 0 NA 1 728830e 01 9146799 1 RP3 510D11 0 020635750 0 0 0 NA 5 558425e 02 10087260 1 RP4 575L21 0 020635750 0 0 0 NA This script outputs array files in the following directory structure e a first subdirectory structure contains pan genomic profile of each array and chromosomic profile of all arrays in the project project name this subdirectory structure is used for Import functions Iproject name array larray name xml chr chr01 xml chr chrY xml e a second subdirectory structure contains chromosomic profile of all arrays in all projects this subdirectory structure is used for Save and Load functions all chr01 larray name xml chrY larray_name xml Qus UIECLOL y SLLU
71. t Alterations Choose Recurrent regions At least 12 out of 30 profiles must share the same alterations 37 Figure 3 42 Recurrent Alterations Results the recurrent alterations are drawn in red for gain green for loss Here there is only one loss region 38 Clustering is a general technique for unsupervised data classification widely used in microarray data_analysis A VAMP function offers the possibility to perform a hierarchical clustering Kaufman and Rousseuwl 1990 on the array CGH profiles see Figure 2 43 606 VAMP V1 4 12 Point View File Views Edit Help 4 CGH KAMP is developped and y A ffy SNPs begiste red by Institut Curie 1 3 3 Transcriptome LO H h A ae Cer 3 ChIP chip P 01i 135 Clustering t Compute Breakpoint Frequency isl Cytogenetic Banding P Sit Diffential Analysis gt an FrAG L A Cancer 33 Genome Alteration d n SE L Signal Histogram h DS d Genome Annotation P 5 Sample Annotations Sir Chromosome Switch P Ga Filter b AA i 1 Sort by d BE i Mis C Sie TA TN TT Figure 3 43 Tools Clustering Compute The user can open a new window of dialog for clustering The clustering can be performed on different variables see Figure 9 44 Probe LogRatio The Probe LogRatio values of the whole genomic profile are used Probe Smoothing The Probe smoothing values i e the results of a segmentation algorithm of the whole genomic profile are us
72. t clicking on this region and then clicking Sort CGH arrays see Figure 4 7 d all the samples with the alteration appear at the top of the panel The same operation can be performed for amplified regions on chromosome 6 and 11 File Views Edit Tools Help EEN Point View Barplot View Curve View DotPlot View Default Color Codes 1 Show Breakpoints Show Smoothing Points Pin up info Show Centromere Show Outliers Hide Size earch EIS Show All Hide All Hightlight Minimal Alterations Hightlight Recurrent Alterations Pin up info Sort CGH arrays Center on region Remove region and landmarks Remove region but not landmarks Edit properties Set color b a Center on mini b Zoom in in X and c View menu Highlight d Sort CGH Arrays mal amplified region Y scale Minimal Alterations at 8022 8023 5 Remove region and landmarks E E Remove region but not landmarks Edit properties Set color Figure 4 7 Visualization of the samples with the amplification at 8q22 8q23 4 3 4 Candidate genes To retrieve the list of genes located in the amplified regions previously identified do the following de Oo A C2 N import in the current view the human gene profile see Figure 4 8 a It will will be displayed at the bottom of the main panel scroll down to the bottom of the main panel click on the
73. tected by any algorithm Hup et al We propose two different approaches to identify such regions of biological interest e Tools Genome Alteration Compute Minimal Alterations are extracted by inter secting the profiles of many tumors and looking for a sufficient number of alterations in the tumors this parameter is set by the user over the smallest possible region of the profile see Figures and 3 39 e Tools Genome Alteration Compute In a given tumor an alteration is bounded by two extremities which can be a breakpoint or a chromosome end when an alteration is present in a sufficient number of tumors with the same extremities it is a recurrent alteration see Figures and 3 42 For both Recurrent Alterations and Minimal Alterations the user has to set the Minimum support required that is the minimum number or percentage of tumors showing the alteration for considering it as significant 34 E a H ka File Views Edit RA Help Keen VAMP is developped and ARNES registered by Institut Curie Transcriptome LOH ChiP chip Clustering Breakpoint Frequency Cytogenetic Banding gt mH Diffential Analysis FrAGL Genome Alteration Signal Histogram Genome Annotation Sample Annotations Chromosome Switch Sort by Misc Figure 3 37 Tools Genome Alteration Compute The user opens a new dialog window to set the parameters for Minimal Alterations Figure 3 38 Minimal Alt
74. terations deselect Gain and Loss to search only for Amplicon Genome Alteration Dialog Figure 4 5 Genome alteration parameters ot Once the search is completed the minimal amplified regions are displayed as vertical blue lines minimal amplified regions are located on chromosomes 6 8 and 11 In order to see the accurate location of the regions with respect to the cytogenetic bandings do as follows see Figure 4 6 1 in the bottom left corner click on Minimap to display the chromosome image with cytoge netic bandings 2 in the main panel mouse over the sample profiles for chromosome 6 8 and 11 and you will see that the minimal amplified regions are highlighted in blue in the minimap panel 400 Chr 8 Human 400 A 413 14 Figure 4 6 Minimap and minimal amplified region at 8022 8823 28 The visualization of the samples which share the minimal amplified regions is available within the interface 1 2 3 SS eee RE 8 3 10 11 12 13 14 15 16 E Sort CGH arrays Center on region at the top of the panel click right on the minimal amplified region at 8422 8423 and center on it see Figure 4 7 a zoom in in the X and Y scale see Figure 4 7 b click on View Current View Highlight Minimal Alterations see Figure 4 7 c a grey box will highlight the samples which have the minimal alteration sort the samples which have the minimal amplified region at 8022 8023 by righ
75. thingLineFG gt lt SmoothingPointFG gt BLACK lt SmoothingPointFG gt lt SmoothingPointWidth gt 2 lt SmoothingPointWidth gt lt TabBG gt WHITE lt TabBG gt lt TabbedPaneFont gt MonoSpaced BOLD 10 lt TabbedPaneFont gt lt ThresholdMaxYFG gt RED lt ThresholdMaxYFG gt lt ThresholdMinYFG gt GREEN lt ThresholdMinYFG gt lt ThresholdPane1BG gt ORANGE lt ThresholdPane1BG gt lt ThresholdPanelButtonBG gt WHITE lt ThresholdPanelButtonBG gt lt ThresholdPanelLabelFont gt SansSerif PLAIN 9 lt ThresholdPanelLabelFont gt lt Threshold_CGH_MaxY gt 2 8 lt Threshold_CGH_MaxY gt lt Threshold_CGH_MinY gt 0 01 lt Threshold_CGH_MinY gt lt Threshold_ChIP chip_MaxY gt 16 0 lt Threshold_ChIP chip_MaxY gt lt Threshold_ChIP chip_MinY gt 0 01 lt Threshold_ChIP chip_MinY gt lt Threshold_SNP_MaxY gt 8 0 lt Threshold_SNP_MaxY gt lt Threshold_SNP_MinY gt 0 1 lt Threshold_SNP_MinY gt lt Threshold_TRSREL_MaxY gt 10 0 lt Threshold_TRSREL_MaxY gt lt Threshold_TRSREL_MinY gt 0 25 lt Threshold_TRSREL_MinY gt lt Threshold_TRS_MaxY gt 5000 0 lt Threshold_TRS_MaxY gt lt Threshold_TRS_MinY gt 10 0 lt Threshold_TRS_MinY gt lt TitlePanelBG gt ffffd0 lt TitlePanelBG gt lt TranscriptomeMergeColorBase gt WHITE lt TranscriptomeMergeColorBase gt lt Utr3FG gt ee00 lt Utr3FG gt lt Utr5FG gt 6600 lt Utr5FG gt lt UtrHeight gt 2 lt UtrHeight gt lt ViewBG gt WHITE lt ViewBG gt lt ZoomPane1BG gt ORANGE lt ZoomPane1BG gt lt
76. token gt lt add gt lt Menultem gt lt Menultem type url title Ensembl CytoView url data target blank token http www ensembl org Homo_sapiens cytoview chr Chr amp amp vc_start lt token gt lt sub gt lt property gt Position lt property gt lt token gt 150000 lt token gt lt sub gt lt token gt amp amp vc_end lt token gt lt add gt 2 lt add gt lt Menultem gt lt Menultem gt lt PropertyElementMenu gt Parameterization of the contextual menu of an object of ProbeSet type how to add an hypertext link lt PropertyElementMenu object DataElement type ProbeSet gt lt Menultem type separator gt lt MenuItem type menu title External Links gt lt Menultem type url title Genecards Viewer url http genecards curie fr cgi genecards cardsearch pl search SourceID target blank MenuItem lt PropertyElementMenu gt Parameterization of the contextual menu of the Minimap how to add an hypertext link lt PropertyElementMenu object MiniMapChr gt lt MenuItem type menu title External Links gt lt Menultem type url title NCBI Map Viewer url http www ncbi nlm nih gov mapview maps cgi 0RG human amp amp MAPS cntg r clone sts genes compxamp CHR Name target blank lt MenuItem gt lt PropertyElementMenu gt lt PropertyElementMenu object MiniMapBand gt lt
77. vailable in the public data sets provided with this distribution Any other tags may be added in the lt Obj gt description They will be listed in the Info Panel of the bottom left frame figure B 3 and will be taken into account by the Search Elements function section 2 2 3 A sample XML file for CGH array data is given in the Annexes see 8 4 Transcriptome array data The following four tags are mandatory for describing transcrip tome probe sets lt ObjectId gt the name of the object lt PosBegin gt start position of the probe set on the genome lt PosEnd gt end position of the probe set on the genome Signal signal value The following fields are optional they provide hypertext links towards public databases within VAMP lt Source gt origin of the object IMAGE GenBank lt SourceID gt object identification for the public database Any other tags may be added in the lt Obj gt description They will be listed in the Info Panel of the bottom left frame figure B 3 and will be taken into account by the Search Elements function section B 2 3 A sample XML file for transcriptome array data is given in the Annexes see 8 5 11 Finally we describe the data format used for adding sample annotation data to molecular profiles Clinical data descriptions are encapsulated as follows lt SampleAdditionalData gt lt ClinicalData gt lt Age gt 72 lt Age gt lt Sex gt Male lt Sex gt
78. w 2 import all the chromosome 6 profiles from the stransky_2006 directory File Import see Figure below 3 once imported select all profiles Edit Select A11 4 load transcriptome profiles associated to the CGH arrays Tools Transcriptome Load 5 start the genome transcriptome correlation analysis Tools Correlation Analysis Compute with default parameters VAMP Import Data janoueix lerosey 2005 kotliarov 2006 leeuw_2004 mosse 2005 nakao 2004 patil 2005 gt pollack 2002 snijders 2001 snijders 2005 stransky 2006 Arrays v Chromosomes L chrO1 chr02 chr03 chr04 2 chr05 i chr06 All arrays A_1033 14 A_1087 1 14 A_1210 14 A_1211 2 14 A_1212 14 A_1333 4 14 A_1343 2 14 A_1352 1 14 A_1379 14 A_1382 2 14 A_1410 14 A_1412 14 A 1413 14 4 FX TR ASA v 4 VY Y Y Y Import data Cancel Refresh Figure 4 10 Importing array CGH profiles A new window opens where correlations are displayed along chromosome 6 the highest correlation is 0 88 and correspond to the 41632 AT probe located at 6p22 Right clicking on this probe allows to have an external link to the Genecards database see Figure 4 11 a this probe correspond to the E2F transcription factor 3 Go back to the previous view with the 196 genome wide profiles and click on Search Elements on the top left panel and do the following see Figure 4 11 b 1 select GeneSy
79. which are displayed in the current view see Figures 3 59 and 2 60 File Views Edit Tools Help CGH b VAMP is developped and Affy SNPs registered by Institut Curie 1 2 3 4 5 5 1 9 m GE dE 3 Transcriptome LOH ChiP chip rerio Clustering ez Breakpoint Frequency Cana Cytogenetic Banding A HKI5 10 Diffential Analysis HO FrAGL A HK19 10 Genome Alteration CA Sa Signal Histogram Compute 4 Related Arrays A A HK27 10 A HK28 10 A HK29 10 A HK340 AHK31 10 A HK36 10 A HK37 10 A HK38 10 Ib ALHK39 10 HK La Chr1 Human 400 Ge 20 A_HK13 10 AO A HK7 10 A_MK8 10 A_HK9 10 A Hep3B 10 A HepG2 10 A SELIO ASSEI2 10 A SF15 10 A_SF17 10 A SF18 10 A SP24 10 A SES 10 A SE30 10 A_SF35 10 A SF4 Hd Genome Annotation Sample Annotations Chromosome Switch Filter Sort by Misc Figure 3 59 Tools Signal Histogram Compute The user can open a new window of display signal histogram view eoe File Views Edit Tools Help ZZ VAMP is developped and registered by Institut Curie 249 208 166 125 083 042 000 O40 O81 123 164 206 247 288 330 371 Point Point View 1 element A CH3 10 A HK1 10 A HK11 10 A_HK12 10 A HK13 10 A HK14 10 A_HK15 10 A HK16 10 A HK18 10 A HK19 10 A HK2 10 A_HK20 10 A_HK21 10 A_HK22 10 A_HK23 10 A HK24 10 A HK27
80. wing files should be modified cgh html configuration xml syscfg xml configuration xml print report xml in order to replace the default path C VAMP with the new path For example let us assume you have copied the VAMP directory into http hosted myHome com html Then replace file C VAMP with http myHome com VAMP Note that the standalone version uses the file protocol whereas the intranet server version uses the http protocol 2 2 2 How to launch VAMP In the case of a standalone version just open the file index html in the VAMP directory and in the case of an intranet server version just open the url http myHome com VAMP 2 2 3 Configuration There are two configuration files in VAMP the administrator configuration file which is the most important and the user configuration file Administrator configuration The main configuration file syscfg xml can be modified by the administrator It contains the initialization of the resources i e access path to the data url address to your favorite public databases cytogenetic banding informations which allows VAMP to be launched correctly The xml data file need to be copied into the root directory defined in the tag lt Parameter key importData baseURL value file yourRootDirectory gt as described below A sample administrator file is given in the Annexes eech 1 it can be modified to customize the contextual menus regarding the information of

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