Inferring transcription factor complexes from ChIP-seq data

Whitington, Tom, Frith, Martin C., Johnson, James and Bailey, Timothy L. (2011) Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Research, 39 15: e98-1-e98-11. doi:10.1093/nar/gkr341

Author Whitington, Tom
Frith, Martin C.
Johnson, James
Bailey, Timothy L.
Title Inferring transcription factor complexes from ChIP-seq data
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2011-08-01
Sub-type Article (original research)
DOI 10.1093/nar/gkr341
Open Access Status DOI
Volume 39
Issue 15
Start page e98-1
End page e98-11
Total pages 11
Place of publication Oxford, U.K.
Publisher Oxford University Press
Language eng
Formatted abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) allows researchers to determine the genome-wide binding locations of individual transcription factors (TFs) at high resolution. This information can be interrogated to study various aspects of TF behaviour, including the mechanisms that control TF binding. Physical interaction between TFs comprises one important aspect of TF binding in eukaryotes, mediating tissue-specific gene expression. We have developed an algorithm, spaced motif analysis (SpaMo), which is able to infer physical interactions between the given TF and TFs bound at neighbouring sites at the DNA interface. The algorithm predicts TF interactions in half of the ChIP-seq data sets we test, with the majority of these predictions supported by direct evidence from the literature or evidence of homodimerization. High resolution motif spacing information obtained by this method can facilitate an improved understanding of individual TF complex structures. SpaMo can assist researchers in extracting maximum information relating to binding mechanisms from their TF ChIP-seq data. SpaMo is available for download and interactive use as part of the MEME Suite (
Keyword DNA-binding sites
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article # e98.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
Institute for Molecular Bioscience - Publications
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