Introduction

We propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK demonstrates better performance compared with existing methods, identifies both positively and negatively selected genes simultaneously, and reports robust results across different experimental conditions. Using public datasets, MAGeCK identified novel essential genes and pathways, including EGFR in vemurafenib-treated A375 cells harboring a BRAF mutation. MAGeCK also detected cell type-specific essential genes, including BCR and ABL1, in KBM7 cells bearing a BCR-ABL fusion, and IGF1R in HL-60 cells, which depends on the insulin signaling pathway for proliferation.

Publications

  1. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
    Cite this
    Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS, 2014-01-01 - Genome biology
  2. Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.
    Cite this
    Li W, Köster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS, 2015-12-01 - Genome biology

Credits

  1. Wei Li
    Developer

  2. Han Xu
    Developer

  3. Tengfei Xiao
    Developer

  4. Le Cong
    Developer

  5. Michael I Love
    Developer

  6. Feng Zhang
    Developer

  7. Rafael A Irizarry
    Developer

  8. Jun S Liu
    Developer

  9. Myles Brown
    Developer

  10. X Shirley Liu
    Investigator

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Summary
AccessionBT001993
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByX Shirley Liu