Using the Genome Browser to Explore Genomics Data
Contents
1. Page Break Preview Ruler V Formula Bar Q is New Window lt Custom Views Gridlines V Headings Arrange All xod 3 Full Screen Message Bar soe EH Freeze Panes 2 L Workbook Views Show Hide Zoom v 5 GE GSM74875 CEL Normalized B G H 1 GE GSM74875 CEL Normalized 2 Chromosc Start End Normalized Probe SetID Entrezid Gene Symbol 3 2 2 02E 08 2 02E 08 0 19958973 226291 at 57679 ALS2 4 chr2 2 02 08 2 02 08 1 905309 1555284_ 57679 ALS2 5 chr2 2 02 08 2 02 08 0 06544447 232184 at 57679 ALS2 6 chr2 2 02E 08 2 02E 08 1 5915208 1560742 at 7 chr2 2 02 08 2 02 08 1 4181561 1560743 a at 8 2 2 02E 08 2 02 08 0 83980584 1552559 a at 65061 PFTK2 9 2 2 02 08 2 02 08 0 52900696 1554826 at 65061 PFTK2 10 chr2 2 02 08 2 02 08 0 14593697 239201 at 65061 PFTK2 11 chr2 2 03 08 2 03E 08 0 3795967 203706 s at 8324 FZD7 12 2 2 03 08 2 03 08 0 2621107 203705 s at 8324 FZD7 13 chr2 2 03 08 2 03 08 1 8460946 1564193 at 105057 3 739061 LOC339809 14 chr2 2 03 08 2 03 08 2 0135744 1556536 at 729224 hCG 2044152 15 2 2 03 08 2 03 08 0 21768475 201317 5 5683 PSMA2 16 2 2 03E 08 2 03E 08 0 106933594 208762 at 7341 SUMO1 17 2 2 03 08 2 03 08 0 23903847 223096_ 51602 58 18 2 2 03 08 2 03 08 0 37582636 235861 at 19 chr2 2 032. Click on any track and drag right left with mouse Summary Panel M IMi N 23 a gt 4 L PaL 07 07 9 90 9 90 9o 9 90 90 92 92 90 Scroll up down mouse wheel E Summar y Panel Spreadsheet E mmm Use right left arrows within any track RE Agilent Technologies Navigation Chromosome Selector Gene Expression of Prostate Cancer 3 Copy Number analysis of Prostate Cancer ix o 3863280 bp A 8 EF 99 25M 99 64M 100 02M 100 41M 100 80M 101 18M 101 57 M 101 36M 102 34M 102 73M 103 11M Copy Number analysis of Prostate Cancer 55 374561 cel Copy Number P nom 11 a nd E zi SS 14 8 Gene Expression of Prostate Cancer Metastatic Normalized Gene Expression of Prostate Cancer Normal Normalized Chromosome chri 247249719bp Region 99256352 103119631 1 22011 LUBMLIULIMIL T _ LL ODE OX C o LER fu UAB A AU efe Re Pep Rip ATO Sy Rufo 24 E summary Panel Spreadsheet 704M of 885N E Agilent Technologies M Navigation Chr Drop down a
3. Using the Genome Browser to Explore Genomics Data uu Shady Fatum n Pr Gene in acid Innen Valuas PA 326 98 e e e adn CHF Etielogy Hon averaged THAT LE 0874567 114807 Hui 5091255 0 023277 Br aa 5 1 i cue ur dr uo Jean Jasinski Ph D 5 Senior Application Scientist ME 1 6 y 201 0 Chromosome chez 212961349 Regan sess xem Normatzed 61923000 0 017506039 3x64 9 4140 FAMIGLIA 61921274 96252927 0152726 55 LJ LE 3 Agilent Technologies a Features of Genome Browser Navigation in Genome Browser Import and Export of Information from Genome Browser RE Agilent Technologies Methylation and Gene Expression Profiling of Prostate Cancer Methylation profiling of prostate cancer GSE 15298 20 prostate cancer tissues Cy5 Pooled reference lymphocyte of age matched healthy men Cy3 Agilent Human 244K CpG Island Array treated like expression array Gene expression profiling of prostate cancer GSE
4. Etiology Select Data Samples Selected items Available Items Samples Selected items G5M374561_cel zip G5M374562_cel zip G5M374563_cel zip G5M374564_cel zip 55 374565 cel zip Available Items Genotype Calls Allele Frequencies Genotype Calls Selected items 5M374571 cel zip Match Case G5M374576 cel zip 5 374580 cel zip 35 374531 cel zip G5M374532 cel zip C Copy Number Confidence 5 374533 cel zip Copy Number Allele Specific Copy Number Log Ratios Parent Specific Copy Number Available Items Select All d Match Case Options of values to plot depends on experiment type 4 Agilent Technologies a Plot Entity Lists in Genome Browser 9166257 bp 07 50 108 01 108 53 103 05M 103 56M 110 08M 110 60M 111 11M 111 63M 112 14 112 66M MU AMT ab ae 904 Bi IEEE mm ae a e 07 50 108 01M A 3M 109 05 E 3166257 108 5 110 08M 110 60M 111 111 63M 112 14M 112 66M Veer S e 0210 Sj Expression profiling in monozygotic twins discordant for bipolar disorder 9527036 T Test p sion profiling in monozygotic tins discordant for bipolar disorder gse T036 T Test paired Bipolar di for dtr Ws
5. 08 2 03 08 0 24602127 210214 s at 659 BMPR2 20 2 2 03 08 2 03 08 0 06939316 209920 at 659 BMPR2 21 chr2 2 03 08 2 03 08 0 062489986 238393 at 22 chr2 2 03E 08 2 03E 08 0 47584152 238516 at 659 BMPR2 23 2 2 03 08 2 03 08 0 3312559 231873 at 659 BMPR2 24 chr2 2 03 08 2 03 08 0 007563591 225144 at 659 BMPR2 25 chr2 2 03E 08 2 03E 08 1 8932452 243186 at 4 gt gt GBrowserSData 2 Ready Agilent Technologies Import and Manage Tracks in Genome Browser Import and Manage tracks Import and Tracks view and manage Features and builds asso Use Ehe left navigator pane to browse exis information in that Folder For example click on genome build Folder BED Format Files are recognized by def gg Delete Organism Delete the org Mew Organism Create nagforganism Mew Build Create new build under tl Caenorhabditis elgg Homo sapiens E73 Mus musculus _ Rattus norvegicus 15 organism Details Information Source Llc Sic Import and Tracks View and manage features and builds assoc Use left navigator pane ta browse exist information in that Folder For example click on genome build Foldey Details Information Delete build 2009 10 14 00 00 00 0 j E E Mus musculus E E Rattus norvegicus New build Features Av
6. 61921274 0 008232927 33662 at 84140 FAM161A 61969267 0 17927206 32594 at 10575 CCT4 0 063627936 40423 at HBP1 0 05286918 4190 1 0 21267247 7360 UGP2 v eoo a e Spreadsheet tab displays data for selected track Search for Entity of interest using value in any Spreadsheet columns Entity is highlighted in Track and Spreadsheet Double click on Entity in Spreadsheet to zoom into that Entity in Genome Browser RE Agilent Technologies Navigation Entity List 1900546 bp 25 55 25 74M 25 93M 26 12M 26 31M 26 50M 25 36M GSM374561_cel Copy Number 25 17M lysis of Prostate Cancer 24 79M 24 98M U Copy Number ana e 4032285 auosouwo445 a e Annotation 4 gt A o Mo a lt _ lt 9 8 pia 2 Gene Expression of Prostate Cancer Metastatic Nor malized gt 2 0 Entity List e Entity Lists can be displayed in Genome Browser and used for navigation of tracks Drag n drop Entity List into Genome Browser Scroll via right left arrows of Entity List track instructs GeneSpring GX to navigate by jumping to next entity in list ES Agilent Technologies Importing and Exporting Information the Genome Browser gene Genes 185250882 168301712 es a ra lt a gt 4 Home Insert Page Layout Formulas Data Review View
7. Chromosome chrz 242951149bp Region 107500544 112666600 m Spreadsheet Expression profiling in monozygotic twins discordant For bipolar disorder gse 70 36 T i Chromosome chr2 242951149bp Region 107500344 112666600 Start End Probe Set ID p value Fl Absolute regulation oe Ua 2 LECHE EM ESSE Spreadsheet Expression profiling monozygotic twins discordant For bipolar disorder gse7036 T Test paired bipolar diso 2 109619010 109619493 220461 at 0 015541807 1 380545 down 344 i 111623996 111628401 1555372 at 0 039952544 1 4747479 down 1001 Start End Probe Set ID p value Fil Absolute regulation Entrez Id Gene Symbal 111528208 111638679 222343 0 02202079 1 2612072 down 1001 105877362 108972260 220048 at 0 02009 1 21133508 down 10913 109619010 109619493 228451 at 0 016541807 1 380545 down 344558 SH3RF3 111623996 111828401 1552372 at 0 039952844 1 4747479 down 10015 BCL2L11 111638205 111638679 222343 at O 02202079 12612072 down 10018 BCL2L11 By default Entities in list are plotted as regions by their genomic coordinates To plot Entities by their list associated values if present Right click gt Edit track properties Rendering Plot Select Histogram Profile or Scatter Data column Select desired column to plot s Agilent Technologies Plot Annotation Data in Genome Browser e Annotations available on the Agilent
8. Server include 1887401 bp 180 76M 180 95 181 14 181 33 181 52 181 70 181 4 Gene Track _ dd eee uii CpG Island Track lt gt ranscript Track bolum pen pem pod m You may also add any kind of annotation tracks that you download from an external source such as UC Santa Cruz or with any annotation file you create OE Agilent Technologies Track Plot Options in Genome Browser 830274 bp 65 7 ghene Annotation gt Lancer G8MT5z28583 CEL Normalize Cancer 5SM1T5z850 CEL THor malize Cancer GSM152861 CEL Normalize Cancer GSM152664 CEL Normalize To choose data plot Right click on track gt Edit Track Properties gt Rendering gt Plot OE Agilent Technologies Track Options for Genome Browser Right click on track gt Change track size e Change size of selected track all tracks or all tracks from the same experiment e Fit all tracks in view Right click on track gt Edit track properties Rename track Apply smoothing e Show label for Entities in track e Change range of y axis Change plot type And more Apply sampling Apply Smoothing Smoothing Window Size E Show Cross Hairs Show Center Line Show labels Apply to all Methylation Analysis of Prostate Cancer Normalized tra
9. 3325 6 benign 6 metastatic prostate cancer 7 primary prostate cancer Affymetrix Human Genome U133 Plus 2 0 Array RE Agilent Technologies Features of Genome Browser el ed hal 97 80 71M 180 76M 180 81M 180 86M 180 30M 180 95 471851 gene Genes v D 4 e 4 Glsland Na ONCE rac 4 lo 2 2 2 4 COOP summary Panel Spreadsheet Spreadsheet BoxWhisker Plot E Spreadshee Mx RE Agilent Technologies 181 00M 181 04M 181 03M 181 14M 181 19M 4 gt d ei Joypajas 2 Flexible and Interactive Genome Browser EDEK gt Cardiogenomics Project Navigato 1 Beta 2 testing Experiments Copy Numbe E Ilumina GE Testing Gene expression in l io Select Data 247249720 wy 447M 98 89M 123 62M 148 34M Samples Available Items Selected items 5 374561 cel zip 5 374562 cel zip 5 374563 cel zip GSM374564 cel zip GSM374565 cel zip 5 Copy Number Prostate x H Samples Interpretations aa Analysis 1 My Favorites 1 Published Images 5 Copy Number Prostate Cancer Cardiogenomics iP Seed t t Cardiogenomics 1 Samples aa Interpretations 0 c4 All Samples S
10. Leave blank to not save Zi Agilent Technologies a Exporting Information in Spreadsheet Chromosome chri 247249719bp Region 0247249719 Marmalized Probe Set ID Entrez Id Gene Symbol 969502 1 2995403 15560477 a at 148338 SAMD11 9624494 0 1951585 202115 s 26155 Noc 2L 964499 1 0693126 1553133 at 26155 Noc 2L oof ve 0 35324466 1555650 at 339451 KLHL 17 890961 13314329 29792_at 339451 300345 8874173 224125 ab 04069 901885 0 593 75985 224501 ab 54308 1 1 0 Find Find Mext Find Previous Summary Panel Right click on Spreadsheet Export as Entity List Creates Entity List in Navigator containing Entities in Spreadsheet Export as Text Creates text tsv file containing Spreadsheet information RE Agilent Technologies Export Images s Multiple Track Image Export Description This view helps you bo choose the required tracks which are to be exported as images On clicking ok all the selected tracks will be exported as separate images while respecting the selection order Inside the Folder you will Find the images of the tracks which are exported a HTML File containing the individual track images in the order they exported and another image For horizontal orientation only combining the individual track images in the order they are exported Select Tracks Available ite
11. ailable Mame Snurce Type miRMA 1 UCSC feature 2 cvtaband UCSC Cyboband Mi Delete Feature New Feature Show Chromosome Information Agilent Technologies Import Tracks for Viewing in Genome Browser Import and Manage tracks Import and Manage Tracks View and manage features and builds associated with an organism using this interface Use the left navigator pane to browse existing organisms builds and Features Click on Folders to import and manage information in that Folder For example click on genome build Folder For an organism to delete add build and delete add Features to that build BED Format Files are recognized by default Import and Manage tracks Import and Manage Tracks View and manage features and b Use the left navigator pane to bro that Folder For example click on genome builc BED Format files are recognized b Delete Build Delete the selected build Delete Build Delete the selected build New Build Create a new build Mew Build Create a new build Mew Feature Import a new Feature under this build Mew Feature Import a new feature under this build 5 2 Caenorhabditis elegans Details w Caenorhabditis elegans Enter Feature Information a Homo sapiens Homo sapiens c r Choose Build E a Eust 8 jUcsc 19 Na Value Delete build E E 0 5 HG19 E Mus musculus 4 Rattus norvegicus Name of Featu
12. cks RE Agilent Technologies Genome Browser Tool Bar Pe DE 61812432 98 89M 105 08 3 52 123 80 M 135 38 M 142 RE Agilent Technologies Merge Tracks in Genome Browser 34648585 bp 38 81M 42 27M 43 74 45 20M 32 57 M 56 13M 39 60M 63 06M 66 33M 69 99M T3 46M Copy Humber Prostate Cancer GSM374561 cal Copy Mumber chr1 38813128 734561712 Data tracks and annotation tracks from Copy Number Track same or different Copy Humber Prostate Cancer GSMS7T4561_ cel Log Ratios chr 138813128 73461712 Experiments can be merged Select multiple tracks ee r OD using Ctrl Select i d 38 81 M 42 27M 56 13M 59 60M 63 06M 66 53M bb Cl from ag Copy Humber Prostate Cancer GSM374561 cel Copy Number Copy Humber Prostate Cancer GSM37T4561_ cel Log Ratios 8813128 G e 5 b ar ag T l o split merged tracks Right click gt Split tracks PER Re RETR IY Re NS Ne o WE Agilent Technologies Density View in Genome Browser 0 0 13 80M 33 50M 33 40 M 73 20M 33 01M 118 81M 138 61M 158 178 22M 138 02M Ss LA DA Coy L Au id H EJ E 1 Copy Humber Analysis of Prostate Cancer GSM374561 ce
13. elect All C Match Case 312432 bp 4 Etiology Type Se Analysis Copy Number Confidence All Entities Copy Number 54 46M 60 64M 73 01M 79 19M 85 37M 91 55M 97 73M 103 91M 110 09M 4 5 allele Specific Copy Number Copy Number Prostate Cancer SSM374565_cel Copy Number Log Ratios Parent Specific Copy Number Filtered on Expression 3 Oneway ANOVA lt Chromosome chr1 2472497 19bp Region 0 247249719 Hot Lis B My Lists summary Panel a 10122195 awosowoyp E summary Panel 421M of 10931 From Menu Views gt Genome Browser Multiple experiments can be displayed in the same Genome Browser Drag and drop experiment into Genome Browser 97 90 90 R2 IR Rk ico nett tm v summary Panel Agilent Technologies Genome Browser Three types of objects can be plotted and viewed in Genome Browser Experiment Data Data can be viewed for individual samples or for conditions Entity List Plot entities in list by any list associated values e g fold change p values etc Annotation Track mport and view annotation tracks in Genome Browser Intensity value is not a list associated value RE Agilent Technologies Plot Experiment Data in Genome Browser g Select Data Interpretation
14. l Eng Ratios 4 b eS bi H H n T a mm 1 Ji HH BH ade H 3 9 Hd E g I H B 1 g H H 144 H H H Li T An H n fl H H n Va r H Copy Number Analysis of Prostate Cancer GS5M374552 cal Ratios EB H B H T _ _ t B T T H T H a B E ES EH L1 bal bal E n Hu bal ba ba LT 0 MH ma L1 Copy Humber Analysis of Prostate Cancer Probesets in Identified Regions Amplification Entity List H 11 n H V H ber Analysis of Prostate Cancer Probesets in Identified Regions Deletion Entity List p j u 11 n i H U H H5 HO HTH p d n 1 ha 2 m ta n M T T T F N H Copy Humber Analysis of Prostate Cancer 653 34563 cel Log Ratios 4 b l H ba H M F ta Fa z H Copw Humber An 4 b 7 Chromosome chra i9B zz430bp Region 19802243 millares 22 Chromosome Setecor _ e Allows you to view all entities in selected track for all chromosomes e Example Entity List obtained from Common Genomic Variant Regions Analysis shows region
15. ms Selected items GE Analysis of Prostate Cancer Benign Normalized GE Analysis of Prostate Cancer f Metastatic prostate cance Image options File Start End File Edit View Favorites Tools Help Back 9 d Search Folders C Program Files agilentiGeneSpringG iimages A Mame 4 Picture Tasks s hri cCytoband 39 png View as a slide show 9 Order prints online Address combined tracks png mg MB Analysis of Prostate Ca GE Analysis of Prostate Ca images html Ruler amp 7 png as Print pictures File and Folder Tasks 6 objects lt 3 Computer To export image for a single track Right click on track gt Export as gt Image To export multiple tracks and Genome Browser components Click on Export Select Track as Image icon from Toolbar e Select tracks to export e Set Image Options for export e Folder containing exported images Individual images of selected tracks Cytoband and Ruler of Genome Browser Entire view as displayed in Genome Browser png and html x Agilent Technologies Thank you for your attention Questions E Agilent Technologies
16. nd Region iih Cardiogenomics Hor mal Hor malized CH I I o 13 Genes o 4 b chr2 242951149bp orc ILE 1912730 amp 63bp P 4 4jchrs 180857866bp chr 170899992 chr 158821424bp Summary Panel chr8a 146274826bp Sly BoxWhisker Plot fife Plot 29 Direct Interactions 29 Home m SC 2I mar s RRR Re ni a 9 uis X Agilent Technologies Navigation Cytoband View and Tracks aaa 040 Cardiogenomicz Normal Normalized 1 T 1111 i MEE pc m Chromosome chrl 247249719bp Region 152404832 183474496 ay HER 1 ELA Ty 23 JU PAP Navigate to region of interest Click drag box in Cytoband view in Summary Panel e Shift drag box in any data or annotation track XE Agilent Technologies Navigation Jump to Entity of Interest by Searching in Spreadsheet of Genome Browser Gene Expression of Prostate Cancer Metastatic Normalized em Affymetrix GeneChip HG LI35 amp v2 T Test unpaired Metastatic vs Normal P lt 0 05 FC gt 2 10 Entity List End Normalized Probe Set ID Entrez Id Gene Symbol ULl2cJUUU U UT212J12c JJUUJ Qu Pearle 61923000 0 017506039 33664 g at 84140 FAM161A
17. re E Rattus norvegicus URE Features Available Mame Source Type Date 16 11 2009 15 27 1 Mus musculus date 2009 10 14 00 00 00 0 1 miRNA UCSC feature File to import Advanced Import Show Chromosome Information Advanced Track Import Step 3 of 3 2 Advanced Track Import Step 1 of 3 Choose Columns Check the data columns to be imported The datatype and marks For the data columns can be changed on this page All the columns checked in the checkbox will be imported If column type is not provided For a column column name will Feature Details Choose the name and other details For Ehe Feature UCSC HG18 of feature miRMAcusEam be used instead Note Chromosome Name Start and End are compulsory columns Choose build C pum Ep Ek pee 9 0 7 URL Date 16 11 2009 15 14 Choose the File to import ettingsipbangvoriDeskEoplR C1 51hgisHomao sapiensmiRmMA ExE Choose template miRNA Column 0 Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 Column 7 track name 7711441 1092347 1092441 MIR1970 0 92347 1092441 1093106 1093195 1 2622 o t 1093106 1093195 1094248 1094330 MIR1068 0 HH 1094248 1094330 4 3467214 MIR2032 0 3467214 lt Save template as
18. s of common variation in Chromosome Selector panel RE Agilent Technologies Navigating within Genome Browser Chromosome chr2 242951149bp Region 202288176 211514160 ah cr P te eos E y m Pela 0 6 0 0 Or Wy So So So Ro Pe To So WHF Safe 9 ETE o r Re o RPP RRB Re RE Agilent Technologies Chromosome Selector 8 1 3 4 5 i E B ES 2 g E EI T un Li c E za ri 5 E D BS B 29 m a H B ES 13 14 15 16 17 s 8 H B amp E H U H EJ L1 H i H H B E Ed ri E3 5 H GeneSpring 11 Genome Browser Navigation Jump to Chr of interest Chr Selector Pane 99 25 99 64M 100 02M 100 41M 100 80M 101 18M 101 57M 3 Copy Number analysis of Prostate Cancer GSM374561 cel Copy Number 101 96M Drop down menu in window Zoom into region of interest Click drag box in Cytoband view in Summary Panel Shift drag box in any data or Gene Expression of Prostate Cancer Normal Normalized a otati O trac e Pan around region of interest Chromosome chri 247249719bp Region 99256352 1031196
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