SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data

Abstract

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that brings together information from a broad range of resources, and provides it in manner particularly useful for genome-scale analyses. SOURCE's GeneReports include aliases, chromosomal location, functional descriptions, GeneOntology annotations, gene expression data, and links to external databases. We curate published microarray gene expression datasets and allow users to rapidly identify sets of co-regulated genes across a variety of tissues and a large number of conditions using a simple and intuitive interface. SOURCE provides content both in gene and cDNA clone-centric pages, and thus simplifies analysis of datasets generated using cDNA microarrays. SOURCE is continuously updated and contains the most recent and accurate information available for human, mouse, and rat genes. By allowing dynamic linking to individual gene or clone reports, SOURCE facilitates browsing of large genomic datasets. Finally, SOURCEs batch interface allows rapid extraction of data for thousands of genes or clones at once and thus facilitates statistical analyses such as assessing the enrichment of functional attributes within clusters of genes. SOURCE is available at http://source.stanford.edu.

Figure 1

SOURCE GeneReport for topoisomerase II alpha (TOP2A). This screenshot depicts an example human GeneReport. Data included for this particular gene include a link to SOURCE CloneReports for ESTs mapping to TOP2A, links to outside databases such as LocusLink and the UCSC Genome Browser, aliases, chromosomal location, a link to SOURCE's microarray gene expression data, the LocusLink descriptive summary, SwissProt functional information, GeneOntology annotations, virtual northern EST expression data, a link to the SOURCE GeneReport for the mouse ortholog of TOP2A, a link to TRASER for upstream sequence retrieval, representative GenBank mRNA accession numbers, and a form for formatting boolean PubMed queries using all of TOP2A's aliases.

Figure 2

SOURCE gene expression tools. (A) SOURCE microarray data display for TOP2A's expression across the cell cycle of HeLa cells. The measurements are displayed as a temporally ordered matrix of gene expression data where rows represent genes (unique cDNA elements) and columns represent experimental samples. Colored pixels capture the magnitude of the response for any gene. Shades of red and green represent induction and repression, respectively. (B) Most highly correlated gene expression neighbours of TOP2A in a dataset of normal human tissues and cell lines. This figure only depicts the top 9 of the 47 neighbours with a minimum Pearson correlation coefficients 0.4. (C) Virtual Tissue Northern Blot for SNAP25 (synaptosomal-associated protein, 25 kD). Relative expression of SNAP25 across a variety of tissues was calculated using EST abundance data. Libraries stemming from neuron-enriched or -related libraries are highlighted in red for emphasis.