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

Reported is a method, genome-wide enrichment of seed sequence (GESS), to analyze primary data from siRNA screens to identify major off-targeted transcripts. Using GESS the authors identify off-targeted transcripts in several screens. 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.