| Title | A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. |
| Publication Type | Journal Article |
| Year of Publication | 2012 |
| Authors | Sigoillot, FD, Lyman, S, Huckins, JF, Adamson, B, Chung, E, Quattrochi, B, King, RW |
| Journal | Nat Methods |
| Volume | 9 |
| Issue | 4 |
| Pagination | 363-6 |
| Date Published | 2012 Feb 19 |
| ISSN | 1548-7105 |
| Keywords | Animals, 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. |
| DOI | 10.1038/nmeth.1898 |
| Alternate Journal | Nat. Methods |
| PubMed ID | 22343343 |
| PubMed Central ID | PMC3482495 |
| Grant List | R56 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 |
