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Modules 6 and 7: Genboree and Epigenome Comparison

Modules 6 and 7: Genboree and Epigenome Comparison. Aleksandar Milosavljevic Epigenomics Data Analysis and Coordination Center (EDACC). Presented at the 2 nd Epigenome Informatics Workshop Houston, Texas, September 10t h 2010. Diversity of Epigenomes. Comparing Epigenomes.

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Modules 6 and 7: Genboree and Epigenome Comparison

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  1. Modules 6 and 7: Genboree and Epigenome Comparison Aleksandar Milosavljevic Epigenomics Data Analysis and Coordination Center (EDACC) Presented at the 2nd Epigenome Informatics Workshop Houston, Texas, September 10th 2010

  2. Diversity of Epigenomes

  3. Comparing Epigenomes

  4. Modules 3, 4, 5

  5. Modules 6, 7

  6. Genboree Workbench and Atlas Gene Browser Roles Users Groups Atlas Gene Browser Access Projects Tools Genboree Workbench Genome-centric databases

  7. Genboree Workbench Genboree Tools>>Workbench

  8. Genboree Workbench

  9. Preliminary Exercises 1. Go to Genboree Tools>>Workbench 2. Expand and shrink Data Selector tree in the Workbench 2. Examine properties in “Details” window by clicking on objects in Data Selector 3. Read about required tool inputs and outputs by clicking on inactive tool icons 4. Activate tool icons by selecting required Input and Output

  10. Comparison of “broad” peaks

  11. Exercise #1: Pairwise epigenome signal comparison Go to Genboree Workbench Drag the following tracks into Input box: Group: EDACC Workshop 2010 Database: EDACC Workshop 2010 Class: 0.6 HDHV_Data     Input Track: meCG:h1_bar Input Track: meCG:imr90_bar Class: GeneModel     Input Track: GeneModel:5’UTR Drag your database into Output box. Run Signal Comparison: Analysis>Epigenomics>SignalComparison Check email for results

  12. Two types of Genboree annotation tracks • HDHV (High Density - High Volume) • Example: go to Genboree Browser and select • Group: EDACC Workshop 2010 • Database: EDACC Workshop 2010 • Class: 0.6 HDHV_Data •     Input Track: meCG:h1_bar • Input Track: meCG:imr90_bar • 2. Regular tracks • Example: Class: GeneModel • Input Track: GeneModel:5’UTR

  13. Using attribute-values for annotations Go to Genboree Browser Group: EDACC Workshop 2010 Database: EDACC Workshop 2010 Class: GeneModel     Input Track: GeneModel:5’UTR Check out many available attributes using Tabular View

  14. Genboree Help and LFF format Click on Genboree “Help?” button in the top right area. Check “Help” entries. Check out “LFF format”. View the documentation of attribute-value pairs.

  15. Exercise #2: Building a query Go to Genboree Workbench Drag your database into output box. Build “KEGG_PATHWAY-repair-5UTR” query:

  16. Exercise #2 (cont’d): Running a query Running a KEGG_PATHWAY-5UTR query: Group: Epigenome Atlas Database: Your Database Drag into Input Data: All Annotations in Database and query “KEGG_PATHWAY-5UTR” Drag into Output Targets: Your Database Run Query

  17. Exercise #3: Atlas similarity search Go to Genboree Workbench Drag the following tracks into Input Data box: Group: Epigenomics Roadmap Repository Database: Data Freeze 1 – Full Repo Class: 06.HDHV Data Input Track: SD:H1 H4Kme3 Drag your database into Output Targets box. Run Atlas Similarity Search: Analysis>Epigenomics>Epigenome Atlas Search Repeat with Input Track: H1 H3K9ac Check email for results (results in about 1 hour)

  18. Exercise #3 (cont’d): Atlas sim. search Hello Aleksandar Milosavljevic,Your searchAtlasSim tool run has completed successfully.Job Summary:    JobID: wbJob-1283968416_700501    Input Track: SD:H1 H3K4me3    The number of targets : 247Result Summary:The top 10 target track matches:    Track Name  Pearson correlation    SD:H1 H3K4me3       1.0    BI:iPS18c H3K4me3 2 0.8233    BI:iPS11a H3K4me3 1 0.8204    SF:H1 H3K4me3 1     0.8161    BI:ESI3 H3K9ac 2    0.816    BI:H1 H3K4me3       0.8121    SF:H1 H3K4me3 2     0.8003    BI:ESI3 H3K4me3 1   0.7998    BI:iPS15b H3K4me3 1 0.792    SD:H1 H3K4me3 3     0.7858....

  19. Exercise #3 (cnt’d): Atlas sim. search Hello Aleksandar Milosavljevic,Your searchAtlasSim tool run has completed successfully.Job Summary:    JobID: wbJob-1284061293_073103    Input Track: SD:H1 H3K9ac    The number of targets : 247Result Summary:The top 10 target track matches:    Track Name  Pearson correlation    SD:H1 H3K9ac        1.0    BI:H1 H3K9ac        0.8528    BI:H1 H3K9ac 1      0.846    BI:iPS15b H3K9ac 1  0.8001    BI:iPS18c H3K9ac 1  0.7698    SF:H1 H3K9ac        0.7673    BI:iPS20b H3K9ac 1  0.7449    BI:H1 H3K4me3 2     0.7351    BI:Pancreas H3K9ac 1        0.7241    BI:ESI3 H3K9ac 1    0.7086....

  20. Exercise #4: Atlas Gene Browser

  21. Exercise #4: Atlas Gene Browser

  22. Exercise #1 (continued): Epigenome comparison Check output track reporting results of comparison in 5’UTR methylation in IMR90 relative to H1. Sort the track by score – note largest decrease in IMR90 relative to H1 (largest negative score) in ODF1 Visualize output track in Genboree browser. Search for ELF3 and visualize increase in IMR90 relative to H1.

  23. Querying to the output of comparisons Example: Find all repair-related genes whose 5’UTR regions are much less methylated in IMR90 than in H1

  24. Genboree and scripting Everything that can be done interactively using the workbench can also be done programmatically, typically using short scripts in programming languages like Perl, Python, or Ruby. This is accomplished through Genboree HTTP-based REST APIs (Application Programming Interfaces). Proof: the Genboree Workbench itself was written using Genboree REST APIs. To learn more, check Genboree Help ( under REST APIs ) – the help is correct but incomplete -- does not document all available functionality. Interested to start using Genboree REST APIs? Attend Andrew Jackson’s talk ( Module 8 )

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