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GREAT improves functional interpretation of cis-regulatory regions

Nature Biotechnology volume 28, pages 495–501 (2010)Cite this article

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Abstract

We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. Applying GREAT to data sets from chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) of multiple transcription-associated factors, including SRF, NRSF, GABP, Stat3 and p300 in different developmental contexts, we recover many functions of these factors that are missed by existing gene-based tools, and we generate testable hypotheses. The utility of GREAT is not limited to ChIP-seq, as it could also be applied to open chromatin, localized epigenomic markers and similar functional data sets, as well as comparative genomics sets.

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Figure 1: Enrichment analysis of a set of cis-regulatory regions.
Figure 2: Binding profiles and their effects on statistical tests.
Figure 3: Distal binding events contribute substantially to accurate functional enrichments of p300 limb peaks.

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Acknowledgements

We thank M. Sirota for an early survey of ontologies, F. Sathira for developing an intermediary core calculation engine, T. Capellini for critical reading of the manuscript, M. Davis and S. Gutierrez for system administration and the communities of ontology developers and curators for providing invaluable data sources. C.Y.M. is supported by a Bio-X graduate fellowship. M.H. is supported by a German Research Foundation Fellowship (Hi 1423/2-1) and the Human Frontier Science Program (fellowship LT000896/2009-l). S.L.C. is a Howard Hughes Medical Institute Gilliam Fellow. A.M.W. is supported by a Stanford Graduate Fellowship. G.B. is a Packard Fellow, Searle Scholar, Microsoft Research Faculty Fellow and an Alfred P. Sloan Fellow. Research was also supported by an Edward Mallinckrodt, Jr. Foundation junior faculty grant and US National Institutes of Health grant 1R01HD059862 to G.B.

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Authors and Affiliations

  1. Department of Computer Science, Stanford University, Stanford, California, USA

    Cory Y McLean, Dave Bristor, Aaron M Wenger & Gill Bejerano

  2. Department of Developmental Biology, Stanford University, Stanford, California, USA

    Dave Bristor, Michael Hiller, Bruce T Schaar & Gill Bejerano

  3. Department of Genetics, Stanford University, Stanford, California, USA

    Shoa L Clarke

  4. Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA

    Craig B Lowe

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  1. Cory Y McLean
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Contributions

C.Y.M. developed the core calculation engine, processed ontologies, analyzed data sets and co-wrote the manuscript. D.B. designed and developed the web application. M.H. added key ontologies and calculated ontology statistics. S.L.C. performed and wrote the SRF analysis. B.T.S. contributed to data set analysis and manuscript writing. A.M.W. guided website design and wrote user documentation. G.B. and C.B.L. devised the different enrichment tests and developed early core calculation engines. G.B. supervised the project and co-wrote the manuscript. All authors edited the manuscript.

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Correspondence to Gill Bejerano.

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Supplementary Note, Supplementary Figures 1–4 and Supplementary Tables 1–46 (PDF 5181 kb)

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McLean, C., Bristor, D., Hiller, M. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 28, 495–501 (2010). https://doi.org/10.1038/nbt.1630

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