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Methods

Discovering functional transcription-factor combinations in the human cell cycle

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G₂-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes.

[Supplemental material is available online at www.genome.org and http://genetics.med.harvard.edu/~zhu/combination.html.]

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3394405.

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