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BIOBASE Knowledge Library: Featuring TRANSFAC & ExPlain

Is your research focused on regulation of gene expression? Do you use microarrays, ChIP-on-chip, or protein arrays? Are you interested in uncovering the biology behind a list of differentially expressed genes? If so, you will want to explore a recent addition to the HSLS molecular biology resources collection, the BIOBASE Knowledge Library (BKL).

BKL is a Web-based bioinformatics suite offering three databases and two DNA sequence analysis tools.

You can search these databases for genes or proteins of interest and retrieve expertly-extracted literature findings on function, mutant phenotype, interactions with other proteins, gene expression, promoter location, transcription factor binding sites in promoter regions, cellular localization, and posttranslational modifications.

TRANSFAC: contains information on transcription factors, their experimentally-verified binding sites, DNA-binding profiles, and regulated genes.

• TRANSPATH: a database on biological pathways that provides information on signaling molecules, metabolic enzymes, second messengers, endogenous metabolytes, miRNAs, and the reactions they are involved in, resulting in a complex network of interconnected chains of reactions and pathways.

• PROTEOME: a collection of six protein databases covering information on yeast, human, mouse, rat, worm, human pathogenic fungi, S. pombe, and G protein-coupled receptors proteins.

The real power of this systems biology-driven product comes from its two software programs.

• MATCH: a tool that helps you locate transcription regulatory elements in your sequence of interest. It uses a library of mononucleotide weight matrices from TRANSFAC. Searches may be limited to a specific taxonomic group (vertebrates, plants, etc.) or to a particular tissue (adipose, muscle, liver, etc.) by selecting the appropriate matrix.

• ExPlain: a novel tool for interpretation of gene expression data. It predicts key regulatory molecules which are the actual cause for observed gene expression changes present in an experimental data set. Utilizing data from the TRANSFAC and PROTEOME databases, promoters of differentially expressed genes are analyzed and specific combinations of transcription factors regulating these genes are identified. Then the TRANSPATH database is used to analyze signal transduction networks present upstream of these transcription factors, thus providing a list of key signaling molecules that may be the potential cause of the observed gene expression profile.

Registration Information
To receive access privileges for the BKL databases and tools, please contact the HSLS Molecular Biology Information Service.

~ Ansuman Chattopadhyay and Carrie Iwema

Posted in the 2008 April 2008 Issue