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Nucleic Acids Res. 2005 Jan 12;33(1):272-9. Print 2005.

Inferring combinatorial regulation of transcription in silico.

Author information

1
Humboldt University, Institute for Theoretical Biology Invalidenstrasse 43, 10115 Berlin, Germany.

Abstract

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.

PMID:
15647509
PMCID:
PMC546154
DOI:
10.1093/nar/gki167
[Indexed for MEDLINE]
Free PMC Article

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