A signal–noise model for significance analysis of ChIP-seq with negative control | Zendy

Xu Han | Zendy; Lusy Handoko | Zendy; Xueliang Wei | Zendy; Chaopeng Ye | Zendy; Jianpeng Sheng | Zendy; ChiaLin Wei | Zendy; Feng Lin | Zendy; WingKin Sung | Zendy

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A signal–noise model for significance analysis of ChIP-seq with negative control

Author(s) -

Xu Han,

Lusy Handoko,

Xueliang Wei,

Chaopeng Ye,

Jianpeng Sheng,

ChiaLin Wei,

Feng Lin,

WingKin Sung

Publication year - 2010

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btq128

Subject(s) - computer science , chip , h3k4me3 , noise (video) , false discovery rate , data mining , machine learning , artificial intelligence , biology , genetics , telecommunications , gene , gene expression , promoter , image (mathematics)

ChIP-seq is becoming the main approach to the genome-wide study of protein-DNA interactions and histone modifications. Existing informatics tools perform well to extract strong ChIP-enriched sites. However, two questions remain to be answered: (i) to which extent is a ChIP-seq experiment able to reveal the weak ChIP-enriched sites? (ii) are the weak sites biologically meaningful? To answer these questions, it is necessary to identify the weak ChIP signals from background noise.

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