Journal Article

Inferring combinatorial regulation of transcription <i>in silico</i>

Nils Blüthgen, Szymon M. Kiełbasa and Hanspeter Herzel

in Nucleic Acids Research

Volume 33, issue 1, pages 272-279
Published in print January 2005 | ISSN: 0305-1048
Published online January 2005 | e-ISSN: 1362-4962 | DOI: https://dx.doi.org/10.1093/nar/gki167

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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.

Journal Article.  4924 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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