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Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

Dong Li, Shan He
doi: https://doi.org/10.1101/056952
Dong Li
School of Computer Science, The University of Birmingham, UK Zhisong Pan, Guyu Hu
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Shan He
School of Computer Science, The University of Birmingham, UK Zhisong Pan, Guyu Hu
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Abstract

Motivation Searching for active connected subgraphs in biological networks has shown important to identifying functional modules. Most existing active modules identification methods need both network structural information and gene activity measures, typically requiring prior knowledge database and high-throughput data. As a pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Searching for modules on WGCN thus has potential values. While traditional clustering based modules detection on WGCN method covers all genes, unavoidable introducing many uninformative ones when annotating modules. We need to find more accurate part of them.

Results We propose a fine-grained method to identify active modules on the multi-layer weighted (co-expression gene) network, based on a continuous optimization approach (AMOUNTAIN). The multilayer network are also considered under the unified framework, as a natural extension to single layer network case. The effectiveness is validated on both synthetic data and real-world data. And the software is provided as a user-friendly R package.

Availability Available at https://github.com/fairmiracle/AMOUNTAIN

Contact s.he{at}cs.bham.ac.uk

Supplementary information Supplementary data are available at Bioin-formatics online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 03, 2016.
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Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Dong Li, Shan He
bioRxiv 056952; doi: https://doi.org/10.1101/056952
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Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Dong Li, Shan He
bioRxiv 056952; doi: https://doi.org/10.1101/056952

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