A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens.

TitleA bioinformatics method identifies prominent off-targeted transcripts in RNAi screens.
Publication TypeJournal Article
Year of Publication2012
AuthorsSigoillot, FD, Lyman, S, Huckins, JF, Adamson, B, Chung, E, Quattrochi, B, King, RW
JournalNat Methods
Volume9
Issue4
Pagination363-6
Date Published2012 Feb 19
ISSN1548-7105
KeywordsAnimals, Base Sequence, Calcium-Binding Proteins, Cell Cycle Checkpoints, Cell Cycle Proteins, Computational Biology, Databases, Genetic, Gene Library, Genome, Humans, Mad2 Proteins, Mice, Repressor Proteins, Reproducibility of Results, RNA Interference, Spindle Apparatus, Transcription, Genetic
Abstract

Because off-target effects hamper interpretation and validation of RNAi screen data, we developed a bioinformatics method, genome-wide enrichment of seed sequence matches (GESS), to identify candidate off-targeted transcripts in primary screening data. GESS analysis revealed a prominent off-targeted transcript in several screens, including MAD2 (MAD2L1) in a screen for genes required for the spindle assembly checkpoint. GESS analysis results can enhance the validation rate in RNAi screens.

DOI10.1038/nmeth.1898
Alternate JournalNat. Methods
PubMed ID22343343
PubMed Central IDPMC3482495
Grant ListR56 GM066492 / GM / NIGMS NIH HHS / United States
R01 GM066492 / GM / NIGMS NIH HHS / United States
1 UL1 RR025758-01 / RR / NCRR NIH HHS / United States
GM66492 / GM / NIGMS NIH HHS / United States
UL1 RR025758 / RR / NCRR NIH HHS / United States