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Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies
Orlov Y.L.; Huss M.; Joseph R.; Xu H.; Vega V.B.; Lee Y.K.; Goh W.S.; Thomsen J.S.; Cheung E.; Clarke N.D.; Ng H.H.
2009-05-18
Source PublicationComputing Frontiers 2009 - Proceedings of the Conference and Co-Located Workshops, CompBio 2009
Pages11-18
AbstractGenome-wide identification of transcription factor binding sites and gene regulatory elements is an important problem of computational genomics. Advances in high-throughput sequencing technologies combined with chromatin immunoprecipitation, such as ChIP-on-chip, ChIP-seq and ChIPPET (Paired-End diTag) allow us to map transcription factor binding sites (TFBS) and analyze mechanisms of gene regulation on the level of the entire genome. Examples include Oct4, Sox2, Nanog and 10 other transcription factors in mouse, and p53, c-Myc, ER, FoxA1 in human. Clustering of multiple binding sites by different TF reveals potential enhancer regions in mammalian genome. We discuss here statistical analysis of data mapping quality, sensitivity and specificity issues of the ChIP-seq TFBS sets and downstream gene expression analysis.
KeywordChIP-seq Gene expression regulation Genome-wide statistics Transcription factor binding sites
DOI10.1145/1531780.1531784
URLView the original
Language英語
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Document TypeConference paper
CollectionUniversity of Macau
AffiliationA-Star, Genome Institute of Singapore
Recommended Citation
GB/T 7714
Orlov Y.L.,Huss M.,Joseph R.,et al. Genome-wide statistical analysis of multiple transcription factor binding sites obtained by ChIP-seq technologies[C],2009:11-18.
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