Inferring combinatorial regulation of transcription in silico | Zendy

N. Bl thgen | Zendy

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Inferring combinatorial regulation of transcription in silico

Author(s) -

N. Bl thgen

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki167

Subject(s) - biology , in silico , computational biology , transcription factor , gene , transcription (linguistics) , dna binding site , genetics , promoter , cis regulatory module , gene ontology , microarray analysis techniques , bioinformatics , gene expression , enhancer , philosophy , linguistics

In this paper, we propose a functional view on the in silico prediction of transcriptional regulation. We present a method to predict biological functions regulated by a combinatorial interaction of transcription factors. Using a rigorous statistic, this approach intersects the presence of transcription factor binding sites in gene upstream sequences with Gene Ontology terms associated with these genes. We demonstrate that for the well-studied set of skeletal muscle-related transcription factors Myf-2, Mef and TEF, the correct functions are predicted. Furthermore, starting from the well-characterized promoter of a gene expressed upon lipopolysaccharide stimulation, we predict functional targets of this stimulus. These results are in excellent agreement with microarray data.

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