PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments | Zendy

Tuomo Hartonen | Zendy; Biswajyoti Sahu | Zendy; Kashyap Dave | Zendy; Teemu Kivioja | Zendy; Jussi Taipale | Zendy

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PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments

Author(s) -

Tuomo Hartonen,

Biswajyoti Sahu,

Kashyap Dave,

Teemu Kivioja,

Jussi Taipale

Publication year - 2016

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/btw448

Subject(s) - nexus (standard) , transcription factor , chip , dna binding site , binding site , computer science , computational biology , software , biology , genetics , embedded system , gene , promoter , programming language , telecommunications , gene expression

Transcription factor (TF) binding can be studied accurately in vivo with ChIP-exo and ChIP-Nexus experiments. Only fraction of TF binding mechanisms are yet fully understood and accurate knowledge of binding locations and patterns of TFs is key to understanding binding that is not explained by simple positional weight matrix models. ChIP-exo/Nexus experiments can also offer insight on the effect of single nucleotide polymorphism (SNP) at TF binding sites on expression of the target genes. This is an important mechanism of action for disease-causing SNPs at non-coding genomic regions.

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