GREAT improves functional interpretation of cis-regulatory regions.
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2010-05-02
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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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McLean, Cory Y, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano, et al. (2010). GREAT improves functional interpretation of cis-regulatory regions. Nature biotechnology, 28(5). pp. 495–501. 10.1038/nbt.1630 Retrieved from https://hdl.handle.net/10161/17406.
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Craig Lowe
Craig Lowe is an Assistant Professor in the Department of Molecular Genetics and Microbiology. His research interests are in understanding how traits and characteristics of humans, and other vertebrates, are encoded in their genomes. He is especially focused on adaptations and disease susceptibilities that are unique to humans. To address these questions, Craig uses both computational and experimental approaches. Craig's recent research has been on differences in how genes are regulated between species, or between different individuals within a species, and how this causes traits to differ. All students in Craig's lab are exposed to an interdisciplinary environment; current lab members have backgrounds in mathematics, computer science, neuroscience, developmental biology, and genetics. Each year Craig teaches one or two courses on rotating topics of: ancient DNA, ethical issues in genomics, and software development for genetic analyses.
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