title: Network analysis of gene essentiality in functional genomics experiments.
abstract: Many genomic techniques have been developed to study gene essentiality genome-wide, such as CRISPR and shRNA screens. Our analyses of public CRISPR screens suggest protein interaction networks, when integrated with gene expression or histone marks, are highly predictive of gene essentiality. Meanwhile, the quality of CRISPR and shRNA screen results can be significantly enhanced through network neighbor information. We also found network neighbor information to be very informative on prioritizing ChIP-seq target genes and survival indicator genes from tumor profiling. Thus, our study provides a general method for gene essentiality analysis in functional genomic experiments ( http://nest.dfci.harvard.edu ).
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
authors.forename: Peng
authors.initials: P
authors.lastname: Jiang
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA.
authors.forename: Hongfang
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
authors.forename: Chongzhi
authors.initials: C
authors.lastname: Zang
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA.
authors.forename: Yinling J
authors.initials: YJ
authors.lastname: Wong
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
authors.forename: Cliff
authors.initials: C
authors.lastname: Meyer
authors.affiliation: Department of Statistics, Harvard University, Cambridge, 200092, China.
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA.
authors.forename: Jon C
authors.initials: JC
authors.lastname: Aster
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA. xsliu@jimmy.harvard.edu.|School of Life Science and Technology, Tongji University, Shanghai, MA, 02138, USA. xsliu@jimmy.harvard.edu.
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D064113:CRISPR-Cas Systems; D002460:Cell Line; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D020043:Genes, Essential; D023281:Genomics / Q000379:methods; D006801:Humans; D009369:Neoplasms / Q000235:genetics / Q000401:mortality; D012984:Software; D016019:Survival Analysis