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Tools and Procedures for Data Collection and Discovery: Beta Cell Genomics

Tools and Procedures for Data Collection and Discovery: Beta Cell Genomics. Elisabetta Manduchi , Emily Greenfest -Allen, Cris Lawrence, Chris Stoeckert University of Pennsylvania Perelman School of Medicine May 1, 2012 BCBC Retreat. What we will cover. Basics

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Tools and Procedures for Data Collection and Discovery: Beta Cell Genomics

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  1. Tools and Procedures for Data Collection and Discovery:Beta Cell Genomics ElisabettaManduchi, Emily Greenfest-Allen, Cris Lawrence, Chris Stoeckert University of Pennsylvania Perelman School of Medicine May 1, 2012 BCBC Retreat

  2. What we will cover • Basics • Getting to Beta Cell Genomics • What you can search • Studies • Genes • Genomic locations • (Gene) Relationships • Transcripts • Tools • Gene list meta-analysis • Genome browser (new version!) • Strategies that highlight key features • Find mouse genes on chromosome 6 whose proximal promoter overlaps with a consensus motif for Ptf1 • Put these in our “basket” • Look at overlap between Ptf1a and Rbpjl peak calls in adult mouse pancreas. • What genes are nearby? • Compare to basket genes • How do they compare to Ptf1a and Rbpjl peak calls in embryonic mouse pancreas? • Saving and sharing your strategies • Discussion/ Additional features • Networks • On gene pages • The Network tab • Relation to “Relationships” • What would make the site more useful

  3. Beta Cell Genomics Mission Statement • Collect, curate, and integrate BCBC-generated functional genomics datasets with relevant BCBC resources and key externally-funded datasets. • Provide dynamic interactive access, data mining, and cross-comparisons to key results and features of these datasets through a web site.

  4. Getting to Beta Cell Genomics

  5. Basics: What you can search

  6. Searching StudiesFind studies in islets where Nkx2-2 did something interesting

  7. Search for genes that are differentially expressed between alpha cells and islets AND that have available BCBC antibodies

  8. Search for genes that are differentially expressed between alpha cells and islets AND that have available BCBC antibodies

  9. Tools • Gene list meta-analysis • Comparing behavior of selected genes • Finding genes with similar behavior

  10. Tools • Genome Browser • Selecting tracks • Custom tracks

  11. BCBC restricted tracks

  12. Changed region to Rbpjl gene

  13. Find mouse genes on chromosome 6 whose proximal promoter overlaps with a consensus motif for Ptf1 • Tutorial available • http://www.betacell.org/content/tutorial/

  14. Find mouse genes on chromosome 6 whose proximal promoter overlaps with a consensus motif for Ptf1

  15. Look at overlap between Ptf1a and Rbpjl peak calls in adult mouse pancreas • Go to study 3994 • Get List of Locations for Ptf1a • Get List of Locations for Rbjl • Run strategy looking for overlap • Co-locate with genes • Look at what the genes are • Are basket genes included? • Compare to embryonic on genome browser • Select tracks and drag and drop to organize • Export picture • Save and share

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