EPConDB: Endocrine Pancreas Consortium Database A web resource of the Beta Cell Biology Consortium Concepts and data used in the web site Overview of web site pages Using EPConDB Four Query Examples Going over http://www.cbil.upenn.edu/EPConDB

Other Microarray Platforms Data In EPConDB PancChips & Other Microarray Platforms mRNA Expression Studies DoTS transcripts (mRNA + EST Transcript Assemblies) TF binding sites Data in EPConDB consists of relating the transcripts on expression arrays to results from expression studies performed using these arrays Also relationships between transcripts/genes with transcription factor binding sites to identify transcription factor target genes Overall, relating transcription factor target genes and their expression Promoter Chip TF Target genes

EPConDB is transcript based and uses DoTS transcripts (DTs) A DoTS Transcript or DT is a consensus sequence generated using ESTs and mRNAs EST + mRNA Assembly Example FoxA2 transcript Assembly alignment view DT sequence

For each gene, e.g., foxA2, there maybe more than one DoTS transcript, possibly representing alternative forms (Genome Browser alignments) * There maybe more than one FoxA2 DoTS transcript since alternative transcripts are possible. Shows additional FoXA2 exon DoTS provides a snap shot of the transcriptional activity at a gene locus

Integrated Websites BCBC EPConDB T1DBase EPConDB is integrated with other web sites, can get to EPConDB from BCBC and T1DBAse web sites Reciprocal links with both web sites Antibody reagent links with BCBC Common gene page with T1DBase and EPConDB uses GBrowse

Overview of EPConDB pages EPConDB Home Page Navigation Bar Has links to EPConDB pages What is on Chips? Queries to quickly find transcripts genes and those associated with Chips Home Page Queries to quickly find transcripts genes and those associated with Chips Navigation Bar has links to other EPConDB web pages What’s New Items about new EPConDB features

Navigation Bar (NavBar) Has links to all different kinds of pages Chips Downloads BLAST Query Transcripts Experiments Analysis Help Can try to go though these pages live before exercises Headings on Query transcript page (all available queries) favor of queries available

Query #1 “Find a Particular Gene” Use Query on Home Page Insert gene name/symbol into gene name text search box, e.g, Foxa2 Click Search Result is list of DTs associated with name Choose or click on mouse Foxa2 transcript DT.488237 to get RNA Page

RNA Page Items on RNA Page and Other RNA View Links (examples) Highlight particular info Gene Expression profile GBrowse (which we saw before)

Detailed Views Gene ExpressionProfile

Query # 2 “Find a list of transcripts with down-regulated expression when FoxA2 is deleted” Goto Query Transcripts Page (use NavBar!) Select Down-Regulated Expression Click on “Submit” on Query Form Have option to change parameters but for now use defaults Query Form

Result Page: 15 transcripts with Down regulated Expression Click on the My Transcripts button to view query History Query Results are saved in your Query History

Query # 3 “Find transcripts expressed in the islet with IPF1 (PDX1) sites in their promoters” uses intersection of two query result sets Goto Query Transcripts Page Click on Predicted Transcription Factor Target Genes Choose IPF1 Click Submit Result Set

Query # 3 - continued * Go to the Query Transcript Page again Click on the Down regulated Expression query choose a different study from list, Affymetrix MOE430v2 vs Mouse PancChip 5.0 comparison Click Submit *

From Result Page for Down Regulated Expression Query, Click on My Transcripts Button Check boxes Click Intersect Intersection Result Click on view to see Result Page

Query # 4 “Find genes with a gata6 and FoxA2 site within 300 base pairs of one another in a promoter region” Binding Site Collection Query Select Analysis Link Click on Submit Binding Site Collection Query Form allows searching for TF binding sites (single or multiple) that are found upstream of transcript genomic alignments Select TF from pull down list of TFs or user defined Can take 15 minutes to an hour to run analysis so look at previously run query and results An Example Search Go to home page Under What’s new, click on FORM link Example form already filled in Click on RESULTS (page generated is Tabular Results) Add Results to History (to find how many of these genes are expressed in islet) Perform intersection with transcripts expressed in islet (should already be in your query history) How many genes do you get from intersection? Use this tf binding site model to search for a particular binding site User (add your own binding site) consensus for binding site, distance constraints

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