Network analysis of gene essentiality in functional genomics experiments

Peng Jiang, Hongfang Wang, Wei Li, Chongzhi Zang, Bo Li, Yinling J. Wong, Cliff Meyer, Jun S. Liu, Jon C. Aster, X. Shirley Liu

Research output: Contribution to journalArticle

25 Scopus citations

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 ).

Original languageEnglish (US)
Article number239
JournalGenome biology
Volume16
Issue number1
DOIs
StatePublished - Oct 30 2015

Keywords

  • CRISPR screen
  • Gene essentiality
  • Network analysis

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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    Jiang, P., Wang, H., Li, W., Zang, C., Li, B., Wong, Y. J., Meyer, C., Liu, J. S., Aster, J. C., & Liu, X. S. (2015). Network analysis of gene essentiality in functional genomics experiments. Genome biology, 16(1), [239]. https://doi.org/10.1186/s13059-015-0808-9