Dataset Information

Discovering homotypic binding events at high spatial resolution.

ABSTRACT:

Motivation

Clusters of protein-DNA interaction events involving the same transcription factor are known to act as key components of invertebrate and mammalian promoters and enhancers. However, detecting closely spaced homotypic events from ChIP-Seq data is challenging because random variation in the ChIP fragmentation process obscures event locations.

Results

The Genome Positioning System (GPS) can predict protein-DNA interaction events at high spatial resolution from ChIP-Seq data, while retaining the ability to resolve closely spaced events that appear as a single cluster of reads. GPS models observed reads using a complexity penalized mixture model and efficiently predicts event locations with a segmented EM algorithm. An optional mode permits GPS to align common events across distinct experiments. GPS detects more joint events in synthetic and actual ChIP-Seq data and has superior spatial resolution when compared with other methods. In addition, the specificity and sensitivity of GPS are superior to or comparable with other methods.

Availability

http://cgs.csail.mit.edu/gps.

SUBMITTER: Guo Y

PROVIDER: S-EPMC2995123 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature

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Publications

Discovering homotypic binding events at high spatial resolution.

Guo Yuchun Y Papachristoudis Georgios G Altshuler Robert C RC Gerber Georg K GK Jaakkola Tommi S TS Gifford David K DK Mahony Shaun S

Bioinformatics (Oxford, England) 20101021 24

<h4>Motivation</h4>Clusters of protein-DNA interaction events involving the same transcription factor are known to act as key components of invertebrate and mammalian promoters and enhancers. However, detecting closely spaced homotypic events from ChIP-Seq data is challenging because random variation in the ChIP fragmentation process obscures event locations.<h4>Results</h4>The Genome Positioning System (GPS) can predict protein-DNA interaction events at high spatial resolution from ChIP-Seq dat ...[more]

PMID: 20966006

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Dataset Information

Discovering homotypic binding events at high spatial resolution.

Motivation

Results

Availability

Publications

Discovering homotypic binding events at high spatial resolution.

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