Back to Search
Start Over
NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities.
- Source :
-
Nucleic acids research [Nucleic Acids Res] 2016 Jun 02; Vol. 44 (10), pp. e100. Date of Electronic Publication: 2016 Mar 14. - Publication Year :
- 2016
-
Abstract
- 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 (http://www.NetDecoder.org) 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.<br /> (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Subjects :
- Algorithms
Alzheimer Disease genetics
Alzheimer Disease metabolism
Breast Neoplasms genetics
Breast Neoplasms metabolism
Databases, Factual
Dyslipidemias genetics
Dyslipidemias metabolism
Female
Gene Regulatory Networks
Humans
Signal Transduction
Computational Biology methods
Protein Interaction Maps
Software
Transcriptome
Subjects
Details
- Language :
- English
- ISSN :
- 1362-4962
- Volume :
- 44
- Issue :
- 10
- Database :
- MEDLINE
- Journal :
- Nucleic acids research
- Publication Type :
- Academic Journal
- Accession number :
- 26975659
- Full Text :
- https://doi.org/10.1093/nar/gkw166