GeNets: a unified web platform for network-based genomic analyses.

Journal: Nature methods
Published Date: Jul 1, 2018

Abstract

Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which to interpret a particular genetic dataset. We present GeNets, a platform in which users can train a machine-learning model (Quack) to carry out these comparisons and execute, store, and share analyses of genetic and RNA-sequencing datasets.

Authors

  • Taibo Li
    Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
  • April Kim
    Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
  • Joseph Rosenbluh
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Heiko Horn
    Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
  • Liraz Greenfeld
    Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
  • David An
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Andrew Zimmer
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Arthur Liberzon
    The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
  • Jon Bistline
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Ted Natoli
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Yang Li
    Occupation of Chinese Center for Disease Control and Prevention, Beijing, China.
  • Aviad Tsherniak
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Rajiv Narayan
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Aravind Subramanian
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Ted Liefeld
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Bang Wong
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Dawn Thompson
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Sarah Calvo
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Steve Carr
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Jesse Boehm
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Jake Jaffe
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Jill Mesirov
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Nir Hacohen
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Aviv Regev
    Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Kasper Lage
    Department of Surgery, Massachusetts General Hospital, Boston, MA, USA. lage.kasper@mgh.harvard.edu.

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