MatBase: A New Transcription Factor Knowledge Base

Genomatix Software GmbH, a privately held company offering software, databases and services aimed at understanding gene regulation at the molecular level has released MatBase, a knowledge base of transcription factors (TF).

It contains genomic TF binding sites and protein binding domains, related literature, more than 27.000 known TF, gene interactions, experimentally verified complexes with other TFs (promoter modules), and weight matrix descriptions for the DNA binding sites of TFs.

In contrast to other available TF databases, each entry in MatBase is thoroughly tested for quality and usability for functional analysis of DNA regulatory regions.

“We have developed our in-house TF database now for more than a decade”, says Kornelie Frech, Genomatix´Head of Biological Databases.

"Quality is essential for all further downstream analyses. Our quality standards were the key to success for MatInspector, the de facto gold standard in gene promoter analysis, used by more than 31,000 scientists around the globe today.

More than 80% of our matrices match less than once in 1000 base pairs of random DNA sequences”, she continues.

MatInspector employs the weight matrix descriptions as contained in MatBase for performing TF binding site search in regulatory DNA sequences. Each single matrix is optimized for a minimum number of false positive results in non regulatory DNA.

MatBase is available stand-alone or in combination with MatInspector, either accessible via the WWW or as local in-house installation.