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

Nat Methods. 2012 Feb 19;9(4):363-6. doi: 10.1038/nmeth.1898.


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

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Calcium-Binding Proteins / genetics
  • Cell Cycle Checkpoints / genetics
  • Cell Cycle Proteins / genetics
  • Computational Biology / methods*
  • Databases, Genetic
  • Gene Library
  • Genome / genetics
  • Humans
  • Mad2 Proteins
  • Mice
  • RNA Interference*
  • Repressor Proteins / genetics
  • Reproducibility of Results
  • Spindle Apparatus / metabolism
  • Transcription, Genetic / genetics*


  • Calcium-Binding Proteins
  • Cell Cycle Proteins
  • MAD2L1 protein, human
  • Mad2 Proteins
  • Repressor Proteins