Pan- and core- network analysis of co-expression genes in a model plant
Abstract
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:
-
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- 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:
- Research Org.:
- Brookhaven National Laboratory (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)
- OSTI Identifier:
- 1390059
- Grant/Contract Number:
- PM-031
- Resource 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
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; Computational biology and bioinformatics; Plant sciences
Citation Formats
He, Fei, and Maslov, Sergei. Pan- and core- network analysis of co-expression genes in a model plant. United States: N. p., 2016.
Web. doi:10.1038/srep38956.
He, Fei, & Maslov, Sergei. Pan- and core- network analysis of co-expression genes in a model plant. United States. https://doi.org/10.1038/srep38956
He, Fei, and Maslov, Sergei. Fri .
"Pan- and core- network analysis of co-expression genes in a model plant". United States. https://doi.org/10.1038/srep38956. https://www.osti.gov/servlets/purl/1390059.
@article{osti_1390059,
title = {Pan- and core- network analysis of co-expression genes in a model plant},
author = {He, Fei and Maslov, Sergei},
abstractNote = {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.},
doi = {10.1038/srep38956},
journal = {Scientific Reports},
number = 1,
volume = 6,
place = {United States},
year = {Fri Dec 16 00:00:00 EST 2016},
month = {Fri Dec 16 00:00:00 EST 2016}
}
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Works referencing / citing this record:
Identification of gene expression logical invariants in Arabidopsis
journal, March 2019
- Pandey, Sonalisa; Sahoo, Debashis
- Plant Direct, Vol. 3, Issue 3
A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization
journal, October 2019
- Alabdullah, Abdul Kader; Borrill, Philippa; Martin, Azahara C.
- Frontiers in Plant Science, Vol. 10
A co-expression network in hexaploid wheat reveals mostly balanced expression and lack of significant gene loss of homeologous meiotic genes upon polyploidization
posted_content, July 2019
- Alabdullah, Abdul Kader; Borrill, Philippa; Martin, Azahara C.
A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization
journal, October 2019
- Alabdullah, Abdul Kader; Borrill, Philippa; Martin, Azahara C.
- Frontiers in Plant Science, Vol. 10
Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana
journal, January 2019
- Liu, Wei; Lin, Liping; Zhang, Zhiyuan
- Planta, Vol. 249, Issue 5
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
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