A detailed understanding of how genes are expressed and regulated in different tissues can help elucidate the molecular mechanisms of tissue development and function. 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 (<2,000) of transcription factors (TFs). These TFs usually work in specific combination to regulate individual genes [2
]. A number of databases have been created to facilitate studies of gene expression and regulation. For example, 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
] are databases that store information about transcriptional regulation. Some databases, such as CGED [9
] and PEDB [10
], allow users to access gene expression information derived from either human cancer tissues or one particular tissue (e.g., prostate). However, for a researcher who is interested in tissue-specific gene regulation and would like to examine possible cis-regulatory elements for a gene, a database dedicated to comprehensive information about tissue-specific gene regulation is desirable.
To address this need, we have developed a new database called TiGER (Tissue-specific Gene Expression and Regulation) based on our previous analyses of tissue-specific genes, TFs and cis-regulatory modules (CRMs) for 30 human tissues [3
]. TiGER should not be confused with the earlier TIGR databases [12
] on regulation in microbes, plants and humans. TiGER provides simple search engines so as to permit the users to visualize or download information through a standard web browser. More specifically, the TiGER database has the following features:
• A large set of data on both tissue-specific genes and tissue-specific transcriptional regulatory elements: The database contains tissue-specific expression profiles for ~20,000 UniGene genes, combinatorial regulation for 7,341 interacting TF pairs, and 6,232 cis-regulatory modules for tissue-specific genes.
• Flexible search capability: The database provides three views (gene view, TF view, and tissue view) to allow users to conveniently retrieve information about genes, TFs or tissues of interest. For example, users can simply type a gene ID (e.g., RefSeq) to retrieve the EST profile and CRM detections. Users can also select a tissue name to retrieve a list of genes preferentially expressed in the tissue.
• Convenient accessibility: The database provides visualizations of the gene expression profiles, TF interactions and CRM detections. Sortable summary tables, links to raw data and links to external databases are also provided for user reference.
The rest of the paper will describe the database content and illustrate the utility of the database in tissue-specific gene regulation.