Using the Genome Browser to Explore Genomics Data Jean Jasinski, Ph.D. Senior Application Scientist Mar. 16, 2010 Agenda Features of Genome Browser Navigation in Genome Browser Import and Export of Information from Genome Browser 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 3325) • 6b benign, i 6 metastatic t t ti prostate t t cancer, 7 primary i prostate t t cancer • Affymetrix Human Genome U133 Plus 2.0 Array Features of Genome Browser Flexible and Interactive Genome Browser Choose samples/conditions and values to plot • From Menu, Views > Genome Browser • Multiple experiments can be displayed in the same Genome Browser – Drag-and-drop experiment into Genome Browser 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, pvalues,, etc.)* ) •Annotation Track – Import and view annotation tracks in Genome Browser *Intensity value is not a list-associated value Plot Experiment Data in Genome Browser Genotype Gene Expression Genomic Copy Number Genotyping Options of values to plot depends on experiment type Plot Entity Lists in Genome Browser • By default, Entities in list are plotted as regions by their genomic coordinates • T To plot l t Entities E titi b by th their i lilist-associated t i t d values l (if present): t) Right-click Ri ht li k > Edit track properties > Rendering > Plot > Select Histogram, Profile, or Scatter > Data column > Select desired column to plot Plot Annotation Data in Genome Browser • Annotations available on the Agilent Server include: -Gene Track -CpG Island Track -Transcript Transcript Track 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. Track Plot Options in Genome Browser Annotation Track Histogram Scatter Plot Profile Plot Region Plot To choose data plot type: Right-click on track > Edit Track Properties > Rendering > Plot Track Options for Genome Browser Right-click on track > Change track size • Change size of selected track, all tracks, or all tracks from the same experiment • Fit all tracks in view Right-click on track > Edit track properties • • • • • • • Rename track Change sampling method Apply smoothing Show label for Entities in track Change range of y-axis Change plot type And more… Genome Browser Tool Bar Zoom in and out Show summary of data across all Chromosomes in Chromosome Selector Panel Set order of tracks Import and delete annotation tracks User manual for Genome Browser Merge Selected Tracks Reset to full view Set orientation of tracks to horizontal or vertical Export image Merge Tracks in Genome Browser Data tracks and annotation tracks from same or different Experiments can be merged Copy Number Track Log Ratio Track Merge tracks 1 and 2 • Select multiple tracks using Ctrl + Select • Click on Merge icon from Genome Browser Toolbar p merged g tracks,, • To split Right-click > Split tracks Density View in Genome Browser 3. Entities in selected track is displayed in Chromosome Selector panel 2. Click on “Show 2 Show density in Chromosome Selector” icon 1. Select track to view density across all chromosomes • • Allows you to view all entities in selected track for all chromosomes Example: Entity List obtained from Common Genomic Variant Regions Analysis shows regions of common variation in Chromosome Selector panel Navigating within Genome Browser GeneSpring GX 11 Genome Browser Navigation • Jump to Chr of interest: – Chr Selector Pane – 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 annotation track • Pan P around d region i off iinterest: t t – Click on any track and drag right-left with mouse – Scroll up-down on mouse wheel – Use right-left arrows within any track Navigation: Chromosome Selector Select Chromosome to view Navigation: Chr Drop-down and Region Enter genomic coordinate to view region of interest Use drop-down drop down menu to select Chromosome to view Navigation: Cytoband View and Tracks Navigate to region of interest: • Click + drag box in Cytoband view in Summary Panel • Shift + drag box in any data or annotation track Navigation: Jump to Entity of Interest by Searching in Spreadsheet of Genome Browser Search for Entity in Spreadsheet • Spreadsheet tab displays data for selected track • S Search h ffor Entity E tit off interest i t t using i value l in i any Spreadsheet S d h t columns l – Entity is highlighted in Track and Spreadsheet – Double click on Entity in Spreadsheet to zoom into that Entity in Genome Browser Spreadsheet S d h t shows h data for selected Track Navigation: Entity List • Entity Lists can be displayed in Genome Browser and used g of tracks: for navigation – Drag-n-drop Entity List into Genome Browser – Scroll via right-left g arrows of Entity List track instructs GeneSpring GX to navigate by jumping to next entity in list Importing and Exporting Information the Genome Browser Import and Manage Tracks in Genome Browser Click on Organism folder to 1) Delete or add new organism and 2) Add New build for chosen organism Organism Build Feature1 Feature2 etc. Click on Build folder to 1) Delete or add new build and 2) Delete or add track features Import Tracks for Viewing in Genome Browser BED format is automatically recognized in GeneSpring. Other formats can be imported through “Advanced Import “ Define columns to import for custom track files Exporting Information in Spreadsheet 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 Export Track Images To export image for a single track: Right click on track > Export as > Right-click Image To export multiple tracks and Genome Browser components: Click on “Export Select Track as Image” icon from Toolbar • Select tracks to export • Set Image Options for export • 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) Thank you for your attention Questions?