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http://www.cbil.upenn.edu/EPConDB
Pizarro, A.1, Pinney, D.1, Crabtree, J.1, Mazzarelli, J.1, Grant, G.1, Le, P.1, Manduchi, E.1, McWeeney, S.1, Scearce, M.2, Brestelli, J.2, Brownstein, B.3, Clifton, S.4, Inoue, H.5, Pape, D.4, Melton, D.6, Permutt, A.5, Kaestner, K.2, Stoeckert, C.2
1Center for Bioinformatics, University of Pennsylvania
2Dept. of Genetics, University of Pennsylvania School of Medicine
3Dept. of Genetics, Washington University in St. Louis School of Medicine
4Genome Sequencing Center, Washington University in St. Louis School of Medicine
5Division of Endocrinology, Metabolism and Diabetes, St. Louis, Missouri, USA , Washington University in St. Louis School of Medicine
6Dept. of Molecuar and Cellular Biology, Harvard University
Contact stoeckrt@pcbi.upenn.edu
Genes expressed in the developing pancreas are the focus of the Endocrine Pancreas Consortium Database (EPConDB) with a special emphasis on islet cells, the endocrine portion of the pancreas. Sources of gene expression data include EST’s from cDNA libraries and microarray experimental data sets (including a pancreatic developmental time course study). Represented sequences include tissue libraries generated by the Consortium members as well as all other dbEST libraries from pancreatic tissues. Novel transcripts identified from these libraries are highlighted. Pancreatic EST’s and microarray experiments were used to design an array that is enriched in genes expressed in pancreatic tissues, the PancChip. The clone set used to make the array is available to the scientific community through NIDDK Biotechnology Centers. A listing of clones present on the PancChip is provided on the site. The EST and microarray data are stored in a relational database that underlies the AllGenes (http://www.allgenes.org) project, leveraging the same query and data analysis efforts as this site. Special features include the ability to search for specific signal transduction pathways, BLAST against the sequence set, and construction of complex Boolean queries of gene information (e.g. chromosomal location, Gene Ontology function, gene trap insertions, keywords, etc.). For example, "What genes with GO function "kinase" that have strong similarity (p<=e-100) to those in the insulin signal transduction pathway are expressed in islet cells?" returns 7 entries. Statistical analysis tools for the gene expression data sets are provided over the web. The tools include data plots, clustering (via XCluster) and the differential expression analysis tool PaGE. The available data sets include several points in the pancreatic developmental time series and the original set of microarray experiments supplied by Consortium members to produce the original version of the PancChip.
Recent developments include the addition of a gene expression experimental data set of pancreatic developmental time series points and gene expression data analysis tools. New queries capabilities include search on GeneCard (http://bioinformatics.weizmann.ac.il/cards) gene names, MGI (http://www.informatics.jax.org/mgihome) gene identifiers and gene trap insertions.
EPConDB is part of the NIDDK-sponsored consortium on "Functional Genomics of the Developing Endocrine Pancreas". We gratefully acknowledge support through NIDDK 56947 and 56954 with cosponsorship from the JDFI.
Category Gene Expression
