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PMID: 17921353 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

An Arabidopsis gene network based on the graphical Gaussian model.

Genome research ·Vol. 17 ·No. 11 ·2007-11-00 ·Pages 1614-25

Ma S, Gong Q, Bohnert HJ

Abstract

We describe a gene network for the Arabidopsis thaliana transcriptome based on a modified graphical Gaussian model (GGM). Through partial correlation (pcor), GGM infers coregulation patterns between gene pairs conditional on the behavior of other genes. Regularized GGM calculated pcor between gene pairs among approximately 2000 input genes at a time. Regularized GGM coupled with iterative random samplings of genes was expanded into a network that covered the Arabidopsis genome (22,266 genes). This resulted in a network of 18,625 interactions (edges) among 6760 genes (nodes) with high confidence and connections representing approximately 0.01% of all possible edges. When queried for selected genes, locally coherent subnetworks mainly related to metabolic functions, and stress responses emerged. Examples of networks for biochemical pathways, cell wall metabolism, and cold responses are presented. GGM displayed known coregulation pathways as subnetworks and added novel components to known edges. Finally, the network reconciled individual subnetworks in a topology joined at the whole-genome level and provided a general framework that can instruct future studies on plant metabolism and stress responses. The network model is included.

MeSH Terms
Arabidopsis/genetics Gene Expression Regulation, Plant Gene Regulatory Networks Genome, Plant Models, Genetic Normal Distribution Oligonucleotide Array Sequence Analysis
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ma Shisong
Physiological and Molecular Plant Biology Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
Gong Qingqiu
Bohnert Hans J
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.6911207
Published
2007-11-00
Epub
2007-00-05
Pages
1614-25
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC2045144
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.6911207 PMC Full Text View journal details
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