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

Nature Methods
Frederic D SigoillotRandall W King

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.

References

May 20, 2003·Nature Biotechnology·Aimee L JacksonPeter S Linsley
Aug 11, 2005·Nucleic Acids Research·Xiaoyu LinYu Shen
Apr 12, 2007·Nature Reviews. Molecular Cell Biology·Andrea Musacchio, Edward D Salmon
Jun 26, 2008·BMC Molecular Biology·Cordula TschuchDaniel Mertens
Jan 1, 2010·Nature Reviews. Drug Discovery·Aimee L Jackson, Peter S Linsley
Apr 7, 2010·Annual Review of Biochemistry·Stephanie MohrNorbert Perrimon
Dec 15, 2010·ACS Chemical Biology·Frederic D Sigoillot, Randall W King

❮ Previous
Next ❯

Citations

Dec 25, 2013·Nature Cell Biology·Christof Fellmann, Scott W Lowe
Jun 19, 2013·The Journal of Cell Biology·Grzegorz NalepaWade Clapp
Sep 4, 2012·Nucleic Acids Research·Ryan L BoudreauBeverly L Davidson
Feb 15, 2013·Journal of Virology·Wondimagegnehu M TeferiDavid H Evans
Aug 13, 2013·The Journal of Clinical Investigation·Grzegorz NalepaD Wade Clapp
Mar 13, 2014·Proceedings of the National Academy of Sciences of the United States of America·Andrea FranceschiniChristian von Mering
Aug 7, 2012·Expert Opinion on Drug Discovery·Susanne Heynen-GenelJonathan Rosen
Sep 15, 2015·Experimental Hematology·Zahi Abdul-SaterGrzegorz Nalepa
Feb 24, 2016·Nature Communications·Bhaskar DuttaIain D C Fraser
Dec 19, 2015·Nature Communications·Hye-Sook LeeSung Wook Chi
Mar 10, 2016·The Journal of Cell Biology·Mayumi IsokaneJan Ellenberg
Mar 1, 2016·Expert Opinion on Drug Discovery·Ioannis K Moutsatsos, Christian N Parker
Oct 12, 2015·DNA Repair·Gina KavanaughDavid Cortez
Oct 14, 2014·Cell·Luke A GilbertJonathan S Weissman
Jul 23, 2014·Plant Biotechnology Journal·Adam M TylerGrantley W Lycett
Jul 30, 2014·Parasite Immunology·E J MarrS T G Burgess
Mar 3, 2015·The FEBS Journal·Ella Hartenian, John G Doench
Apr 17, 2016·Methods : a Companion to Methods in Enzymology·Xavier Bofill-De Ros, Shuo Gu
May 31, 2014·Nucleic Acids Research·Michael HannusGunter Meister
Dec 24, 2014·BMC Genomics·Pauli RämöChristoph Dehio
May 20, 2015·Military Medical Research·Xiao Yang
Jul 3, 2013·Seminars in Cancer Biology·Jennifer L WilsonDouglas A Lauffenburger
Nov 28, 2014·Nucleic Acids Research·Aaron A DiazJun S Song
Jun 18, 2016·Integrative Biology : Quantitative Biosciences From Nano to Macro·Jennifer L WilsonDouglas A Lauffenburger
Dec 16, 2016·Nature Communications·Ronni S PedersenClaudia Lukas
Aug 29, 2014·Journal of Biomolecular Screening·Myles FennellRalph J Garippa
Jun 27, 2017·Nature Reviews. Genetics·Nigel J O'NeilPhilip Hieter

❮ Previous
Next ❯

Methods Mentioned

BETA
transfections
transfection
PCR

Software Mentioned

Martview
siNoPhenNoMatch
MATLAB Compiler Runtime ( MCR )
siNoPhenMatch
siPhenNoMatch
Linux
Excel
Spotfire DecisionSite
Mac OS
Ensembl

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.