NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities

Nucleic Acids Res. 2016 Jun 2;44(10):e100. doi: 10.1093/nar/gkw166. Epub 2016 Mar 14.


The sequential chain of interactions altering the binary state of a biomolecule represents the 'information flow' within a cellular network that determines phenotypic properties. Given the lack of computational tools to dissect context-dependent networks and gene activities, we developed NetDecoder, a network biology platform that models context-dependent information flows using pairwise phenotypic comparative analyses of protein-protein interactions. Using breast cancer, dyslipidemia and Alzheimer's disease as case studies, we demonstrate NetDecoder dissects subnetworks to identify key players significantly impacting cell behaviour specific to a given disease context. We further show genes residing in disease-specific subnetworks are enriched in disease-related signalling pathways and information flow profiles, which drive the resulting disease phenotypes. We also devise a novel scoring scheme to quantify key genes-network routers, which influence many genes, key targets, which are influenced by many genes, and high impact genes, which experience a significant change in regulation. We show the robustness of our results against parameter changes. Our network biology platform includes freely available source code ( for researchers to explore genome-wide context-dependent information flow profiles and key genes, given a set of genes of particular interest and transcriptome data. More importantly, NetDecoder will enable researchers to uncover context-dependent drug targets.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Alzheimer Disease / genetics
  • Alzheimer Disease / metabolism
  • Breast Neoplasms / genetics
  • Breast Neoplasms / metabolism
  • Computational Biology / methods*
  • Databases, Factual
  • Dyslipidemias / genetics
  • Dyslipidemias / metabolism
  • Female
  • Gene Regulatory Networks
  • Humans
  • Protein Interaction Maps*
  • Signal Transduction
  • Software*
  • Transcriptome*