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Assessing Computational Steps for CLIP-Seq Data Analysis
Joint Authors
Shyr, Yu
Liu, Qi
Zhong, Xue
Madison, Blair B.
Rustgi, Anil K.
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-11
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
RNA-binding protein (RBP) is a key player in regulating gene expression at the posttranscriptional level.
CLIP-Seq, with the ability to provide a genome-wide map of protein-RNA interactions, has been increasingly used to decipher RBP-mediated posttranscriptional regulation.
Generating highly reliable binding sites from CLIP-Seq requires not only stringent library preparation but also considerable computational efforts.
Here we presented a first systematic evaluation of major computational steps for identifying RBP binding sites from CLIP-Seq data, including preprocessing, the choice of control samples, peak normalization, and motif discovery.
We found that avoiding PCR amplification artifacts, normalizing to input RNA or mRNAseq, and defining the background model from control samples can reduce the bias introduced by RNA abundance and improve the quality of detected binding sites.
Our findings can serve as a general guideline for CLIP experiments design and the comprehensive analysis of CLIP-Seq data.
American Psychological Association (APA)
Liu, Qi& Zhong, Xue& Madison, Blair B.& Rustgi, Anil K.& Shyr, Yu. 2015. Assessing Computational Steps for CLIP-Seq Data Analysis. BioMed Research International،Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1054585
Modern Language Association (MLA)
Liu, Qi…[et al.]. Assessing Computational Steps for CLIP-Seq Data Analysis. BioMed Research International No. 2015 (2015), pp.1-10.
https://search.emarefa.net/detail/BIM-1054585
American Medical Association (AMA)
Liu, Qi& Zhong, Xue& Madison, Blair B.& Rustgi, Anil K.& Shyr, Yu. Assessing Computational Steps for CLIP-Seq Data Analysis. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1054585
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1054585