Pooled shRNA screenings: computational analysis.
Genome-wide RNA interference screening has emerged as a powerful tool for functional genomic studies of disease-related phenotypes and the discovery of molecular therapeutic targets for human diseases. Commercial short hairpin RNA (shRNA) libraries are commonly used in this area, and state-of-the-art technologies including microarray and next-generation sequencing have emerged as powerful methods to analyze shRNA-triggered phenotypes. However, computational analysis of this complex data remains challenging due to noise and small sample size from such large-scaled experiments. In this chapter we discuss the pipelines and statistical methods of processing, quality assessment, and post-analysis for both microarray- and sequencing-based screening data.
Department of Biomedical Informatics, Columbia University, New York, NY, USA.
Jiyang
J
Yu
Preeti
P
Putcha
Andrea
A
Califano
Jose M
JM
Silva
D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D034741:RNA, Small Interfering / Q000235:genetics*
D034741:RNA, Small Interfering