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Title: Pan- and core- network analysis of co-expression genes in a model plant

Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. Some studies involved construction of coexpression networks, a popular technique used to identify groups of co-regulated genes, to infer unknown gene functions. One approach is to construct a single coexpression network by combining multiple expression datasets generated in different labs. We advocate a complementary approach in which we construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications. To this end we reanalyzed public expression data. To describe this collection of networks we introduced concepts of ‘pan-network’ and ‘core-network’ representing union and intersection between a sizeable fractions of individual networks, respectively. Here, we showed that these two types of networks are different both in terms of their topology and biological function of interacting genes. For example, the modules of the pan-network are enriched in regulatory and signaling functions, while the modules of the core-network tend to include components of large macromolecular complexes such as ribosomes and photosynthetic machinery. Our analysis is aimed to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.
Authors:
 [1] ;  [2]
  1. Brookhaven National Lab. (BNL), Upton, NY (United States)
  2. Brookhaven National Lab. (BNL), Upton, NY (United States); Univ. of Illinois, Champaign, IL (United States). Dept. of Bioengineering; Univ. of Illinois, Champaign, IL (United States). Carl R. Woese Inst. for Genomic Biology; Univ. of Illinois, Champaign, IL (United States). National Center for Supercomputing Applications
Publication Date:
Grant/Contract Number:
PM-031
Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Research Org:
Brookhaven National Lab. (BNL), Upton, NY (United States); Univ. of Illinois, Champaign, IL (United States). Dept. of Bioengineering; Univ. of Illinois, Champaign, IL (United States). Carl R. Woese Inst. for Genomic Biology; Univ. of Illinois, Champaign, IL (United States). National Center for Supercomputing Applications
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; Computational biology and bioinformatics; Plant sciences
OSTI Identifier:
1390059