Abstract
BackgroundUnderstanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation.ResultsThe recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation). The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM) detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes.ConclusionWe have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at [1].
Highlights
Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question
DbEST [4] is a database of expressed sequence tags (ESTs) from a number of organisms; GNF SymAtlas [5] and BodyMap [6] are databases that store human and mouse tissue gene expression profiles; TRANSFAC, TRANSCOMPEL and TRED [7,8] are databases that store information about transcriptional regulation
We have developed a new database called TiGER (Tissue-specific Gene Expression and Regulation) based on our previous analyses of tissue-specific genes, transcription factors (TFs) and cis-regulatory modules (CRMs) for 30 human tissues [3,11]
Summary
Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. The approximately 25,000 genes in the human genome demonstrate dramatic diversity in terms of expression levels, both temporally and spatially Despite this diversity, the expression of all genes is controlled by a relatively small number (
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