dCLIP: A computational approach for comparative CLIP-seq analyses

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at http://qbrc.swmed.edu/software/.

Original languageEnglish (US)
Article numberR11
JournalGenome Biology
Volume15
Issue number1
DOIs
StatePublished - 2014

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RNA-binding proteins
RNA-Binding Proteins
RNA
protein
Software
photosynthetically active radiation
methodology
software
Proteins
proteins
Datasets
method
comparison

ASJC Scopus subject areas

  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

dCLIP : A computational approach for comparative CLIP-seq analyses. / Wang, Tao; Xie, Yang; Xiao, Guanghua.

In: Genome Biology, Vol. 15, No. 1, R11, 2014.

Research output: Contribution to journalArticle

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