EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes

Abstract

EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.

Figure 1

Concepts and data used in the EPConDB web site. DoTS Transcripts, which are consensus sequences generated by the assembly of ESTs and mRNAs, are associated with elements on microarray platforms based upon their GenBank accession numbers and RefSeqs. Using the arrays, gene expression is determined under multiple experimental conditions. For the PromoterChip, the tiles are assigned DoTS transcripts based upon Entrez Genes. Transcription factor binding site predictions are made in regions conserved between human and mouse that are in or near a PromoterChip tile. Using the PromoterChip, binding sites can be determined experimentally and employed to validate binding site predictions. Overall, the relationship between a gene, its transcriptional regulation and expression under various conditions can be examined. The colored lines represent sequences used to create a DoTS transcript, black lines represent mRNAs or RefSeqs, grey lines ESTs, red lines represent annotated 5′ ESTs and blue lines annotated 3′ ESTs.

Figure 2

(A) The results page from a query for transcripts with Down regulated Expression in total pancreas as compared with islet tissue having a fold change in expression between 8-fold and 10-fold and a PaGE confidence of 0.9. Twenty-nine transcripts, including a transcript for the gene, Isl1, ISL1 transcription factor, LIM/homeodomain (islet 1), were returned from the query. (B) The transcript page for DT.489821, a DoTS transcript associated with the gene, Isl1. On the transcript page, annotations are displayed including a link to the T1DBase/EPConDB Gene Page and links to the T1DBase Genome Browser. Links to other views for the transcript such as Protein features, EST anatomy and Expression Profile are also available. (C) The Expression Profile link displays gene expression profiles derived from expression studies. Clicking on an individual profile displays the graph and additional information about the study. (D) The T1DBase GBrowse view shows the transcript aligned to the genome. Other views include the BCBC PromoterChip elements and predicted transcription factor binding sites.