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.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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Animals
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Base Sequence
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Calcium-Binding Proteins / genetics
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Cell Cycle Checkpoints / genetics
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Cell Cycle Proteins / genetics
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Computational Biology / methods*
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Databases, Genetic
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Gene Library
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Genome / genetics
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Humans
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Mad2 Proteins
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Mice
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RNA Interference*
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Repressor Proteins / genetics
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Reproducibility of Results
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Spindle Apparatus / metabolism
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Transcription, Genetic / genetics*
Substances
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Calcium-Binding Proteins
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Cell Cycle Proteins
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MAD2L1 protein, human
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Mad2 Proteins
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Repressor Proteins