EPConDB

1. EPConDB A web resource of theBeta Cell Biology Consortium http://www.cbil.upenn.edu/EPConDB

2. Introduction • The EPConDB website provides an integrated view of pancreas- and islet-related gene annotation, expression and regulation data. • Data in EPConDB • Browsing Individual Genes • Working with Gene Lists

3. The Data in EPConDB • Science-driven bioinformatics resource • Composed of heterogeneous information • Maximal cross-talk between types of information Microarrays Methods General Information News Help Downloads EPConDB Research Resources Data Tools BLAST Expression experiments TFBS search Expression profiles Query History Up/down regulated genes Reportmaker ChIP experiments T1DBase genome browser DoTS transcripts Predicted TFBS T1DBase gene pages

4. EPConDB Current Data Content DoTS Transcripts/Genes 940,837 human DoTS transcripts 57,382 are associated with 22,268 unique Entrez genes 22,630 GeneCard genes 746,668 mouse DoTS transcripts 60,931 are associated with 33,276 unique Entrez genes 26,580 MGI genes Expression Data Sets 32 pancreas-related expression data sets contributed by 24 different groups 5 private studies (BCBC viewable) 5 tissue expression surveys (include pancreas and/or islet) 3 expression studies in progress 11 lists of differentially expressed genes from studies 30 studies have gene expression profiles Chromatin IP Data Sets 1 ChIP-on-Chip study 2 lists of TF target genes Predicted Human binding sites - 70,100 Predicted Mouse binding sites - 72,921 2 ChIP-on-Chip studies in progress

5. Home Page • BCBC links • Main navigation bar • Find Gene • By Name • Expression profiles • On arrays • Find gene by sequence

6. Three Integrated Websites Beta Cell Research Informatics Pancreas Functional Genomics Type 1 Diabetes Genetics & Genomics BetaCell.org EPConDB T1DBase.org • Reagents, e.g. Antibodies • Reciprocal links to • both web sites • Gene page & • Genome Browser

7. Finding Individual Genes Queries to quickly find transcripts for genes FoxA2 Transcripts Enter gene symbol or name and click Search. Finds three transcripts from mouse or human genes. Click on DoTS ID to see summary view for that transcript.

8. Transcript Information

9. Expression Profiles • EPConDB contains many pancreas- or islet-related studies. • Very detailed information is easily visualized for each study.

10. Working with Gene Lists Browse lists of genes differentially regulated in mRNA studies. Follow Experiments link in nav bar.

11. Experiments Page • Lists 32 mRNA expression experiments loaded into EPConDB. • Categorized and selectable by experimental design • Links to • Study details • 11 lists of differentially expressed genes (Analysis Result Link) • 1 ChIP-on-Chip experiment with gene lists • RSS link can provide a nice searchable, sortable view. • Display browser specific • Use to update studies displayed at betacell.org

12. Differentially Expressed Genes Analyzed with PaGE. May be multiple analyses for a study. Sortable by confidence or fold change. Links to analysis details. Red is up Green is down Grant G.R., Liu J., Stoeckert C.J.Jr. (2005) A practical false discovery rate approach to identifying patterns of differential expression in microarray data, Bioinformatics 11, 2684-2690.

13. Querying for Gene Lists Browsing genes is nice but you can do more To make the data more useful, EPConDB provides the ability to work with gene lists using queriesandquery history. These tools provide you the ability to generate lists of genes matching your criteria to identify candidate genes for your research.

14. Create a Gene List Which human genes have promoters bound by HNF1alpha in the islet and have a predicted HNF1alpha site in their promoter? Genes with promoters bound by HNF1alpha in the islet EPConDB does not have this query … but … it does have two simpler queries we can combine. Genes with predicted HNF1alpha sites in promoter

15. Gene List #1 Which human genes have promoters bound by HNF1alpha in the islet? Go to the Query Transcripts Page via Navbar. Click on the Query TF Target Genes identified by genome-wide location analysis (ChIP-Chip) Choose a TF from the list, ‘Binding Sites for HNF1alpha’ Adjust fold-change and p-value if desired Click Submit

16. Gene List #2 Which human genes have a predicted HNF1alpha site in their promoter? • Go to the Query Transcripts Page using the Navbar. • Click on the Predicted Transcription Factor Target Genes query. • Select HNF1 (Tcf1) and human genome from the menus • Click Submit • TFBS predicted on conserved regions of promoter in both Hs and Mm. • See methods page to see details and logos of TFBS PWM motifs. • Connected DTs to all TFBS within 1KB of start site.

17. Intersect Gene Lists with History Page Click on the ‘My transcripts’ button to go to the history page. Check boxes With the query history page you can create unions, intersections, and subtract gene lists from each other. You can also delete unwanted gene lists. ClickIntersect button IntersectionResult Click on view to see Result Page or Download

18. Combined Gene Lists Which human genes have promoters bound by HNF1alpha in the islet and have a predicted HNF1alpha site in their promoter? 218 (transcripts) Genes with promoters bound by HNF1alpha in the islet Two simple queries we combined. Result page with 27 transcripts and their corresponding genes. 27 Genes with predicted HNF1alpha sites in promoter 2912 (transcripts)

19. Result Page Gene List Links to DT, Gene, Expression profiles, and genome browser.

20. Summary for this part of the talk • We have covered: • What data EPConDB contains. • How to browse info for individual genes. • How to browse lists of differentially expressed genes. • Gene list queries. How to combine lists to create gene lists that meet your criteria, e.g, genes with promoters bound by HNF1alpha in islet • Visit us at our poster

21. Future EPConDB Site Plans • New web site design in progress • User input will guide development of new site to make site easier to use and navigate • Let us know what you think at poster, please use meeting as opportunity to talk with us • What web site features/views should be maintained? • Sharing logins, BCBC web site and EPConDB

22. Mock ups Home Query Transcripts

23. Planned Functional Genomics Study Pages on betacell.org Abstract from Hardy et al. Mol. Endocrinol. 2006: Recent advances in functional genomics afford the opportunity to interrogate the expression profiles of thousands of genes simultaneously and examine the function ofthese genes in a high throughput manner. In this study, we describe a rational and efficient approach to identifying novel regulators of insulin secretion by the pancreatic beta cell. Computational analysis of expression profiles of several mouse and cellular modelsof impaired insulin secretion identified 373 candidate genes involved in regulation of insulin secretion. Using RNA interference, we assessed the requirements of ten of these candidates and identified four genes (40%) as being essential for normal insulinsecretion. Among the genes identified was short-chain L-3-hydroxyacyl-CoAdehydrogenase (Hadhsc), which encodes SCHAD, an enzyme of mitochondrial oxidation of fatty acids whose mutation results in congenital hyperinsulinism. RNAi mediated gene suppression of Hadhsc in insulinoma cells and primary rodent islets revealed enhanced basal but normal glucose stimulated insulin secretion. This increase in basal insulin secretion was not attenuated by opening of the KATP channel with diazoxide,suggesting that SCHAD regulates insulin secretion through a KATP channel independent mechanism. Our results suggest a molecular explanation for the hyperinsulinemiahypoglycemic seen in patients with SCHAD deficiency. • Proposed to contain key information from • information already existing in EPConDB and • supplemented with manual annotations (e.g., goal, experimental paradigms, genes of interest, take home message) • Title, authors, date, etc… • Summary, with biological relevance • Lists of up/down-regulated genes • Downloads of raw/analysis data • Links to more detail at EPConDB/RAD/PAGE • We ask for your feedback. What do you want • on these pages? J.-P. Cartailler

24. Data Sets and EPConDB Experiments in future EPConDB releases: • Three public microarray data sets (published) • Petri, A. et al. “The effect of neurogenin3 deficiency on pancreatic gene expression • in embryonic mice.” J Mol Endocrinol. 2006 37:301-16. • Liu,Y. et al. “Activation of the Reg family genes by pancreatic-specific IGF-I gene deficiency • and after streptozotocin-induced diabetes in mouse pancreas.” Am J Physiol Endocrinol Metab. • 2006 291:E50-8. • Sherwood, R.I. et al. “Prospective isolation and global gene expression analysis of definitive • and visceral endoderm.” Dev Biol. 2007 304:541-55. • BCBC experiments that become public • Expression data, Chromatin IP binding data • What data sets would you like to see included in EPConDB • or are missing? • What can you contribute to EPConDB to increase the visibility • and thus the value of your data?

25. Microarray analysis on E8.25 definitive and visceral endoderm Melton Group Data analysis/spreadsheet available Go to http://www.betacell.org/ Click on Resources > Data Resources > Research Data Raw data is also being provided and will be annotated/loaded into EPConDB J.-P. Cartailler

26. Experiments in EPConDB are: • Easily submitted to ArrayExpress for you • Included on the EPConDB Experiments page • Used for Gene Expression Profiles • Used to create Gene Lists Extend the analysis to meet your criteria and refine your list of genes Having many experiments in EPConDB will allow for comparisons among data sets.

27. Data Set Submissions • Simple process of submitting your data • Contact us about your data set • use email link or contact us directly • Provide initial experiment description • We create a spread sheet for you • Review your completed spread sheet • Place your data files on our download site A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Tim F. Rayner et al. (2006) BMC Bioinformatics, 7, 489

28. EPConDB Data Submission Step 1: The Sample Submission form provides basic information about your experiment. You fill this out. (4 sections) Step 2: We complete the form and send it back to you for review.

29. Also, review the automatically generated graph of your experiment. (You may be asked to answer some final questions or provide missing details at this step.) Step 3: Upload your data files (.gpr, .cel, .txt) onto our secure ftp site. Step 4: (Optional): Login and view your finalized experiment prior to an EPConDB release (this requires a temporary password).

30. Acknowledgements Nat Goodman & Luc Smink • Barry Healy • Erin Hulbert • Burak Kutlu • James Allen • Victor Cassen CBIL Stoeckert Lab • John Brestelli • Junmin Liu • Jonathan Schug • Elisabetta Manduchi • Joan Mazzarelli BCBC - Mark Magnuson • J.-P. Cartailler • Christian Shaffer • Robert McClellan • Lisa Rouse Functional Genomics Core • Klaus Kaestner • Peter White Funding • NIDDK • JDRF We thank all of the labs who have already contributed data.