Discovering homotypic binding events at high spatial resolution
Discovering homotypic binding events at high spatial resolution
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DOI：
10.1093/bioinformatics/btq590
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发表时间：
2010-12-15
期刊：
影响因子：
5.8
通讯作者：
Mahony, Shaun
中科院分区：
文献类型：
--
作者：
Guo, Yuchun;Papachristoudis, Georgios;Mahony, Shaun
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.
