title: A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens.
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.
authors.affiliation: Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Frederic D
authors.initials: FD
authors.lastname: Sigoillot
authors.forename: Susan
authors.initials: S
authors.lastname: Lyman
authors.forename: Jeremy F
authors.initials: JF
authors.lastname: Huckins
authors.forename: Britt
authors.initials: B
authors.lastname: Adamson
authors.forename: Eunah
authors.initials: E
authors.lastname: Chung
authors.forename: Brian
authors.initials: B
authors.lastname: Quattrochi
authors.forename: Randall W
authors.initials: RW
authors.lastname: King
mesh_terms: D000818:Animals; D001483:Base Sequence; D002135:Calcium-Binding Proteins / Q000235:genetics; D059447:Cell Cycle Checkpoints / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015723:Gene Library; D016678:Genome / Q000235:genetics; D006801:Humans; D064246:Mad2 Proteins; D051379:Mice; D034622:RNA Interference; D012097:Repressor Proteins / Q000235:genetics; D015203:Reproducibility of Results; D008941:Spindle Apparatus / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D002135:Calcium-Binding Proteins; D018797:Cell Cycle Proteins; C577697:MAD2L1 protein, human; D064246:Mad2 Proteins; D012097:Repressor Proteins