In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean.

ABSTRACT: Sequence-specific DNA-binding transcription factors (TFs) are often termed as 'master regulators' which bind to DNA and either activate or repress gene transcription. We have computationally analysed the soybean genome sequence data and constructed a proper set of TFs based on the Hidden Markov Model profiles of DNA-binding domain families. Within the soybean genome, we identified 4342 loci encoding 5035 TF models which grouped into 61 families. We constructed a database named SoybeanTFDB (http://soybeantfdb.psc.riken.jp) containing the full compilation of soybean TFs and significant information such as: functional motifs, full-length cDNAs, domain alignments, promoter regions, genomic organization and putative regulatory functions based on annotations of gene ontology (GO) inferred by com

SUBMITTER: Mochida K 

PROVIDER: S-EPMC2780956 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature