DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Co-expression networks for plant biology: why and how

Journal Article · · Acta Biochimica et Biophysica Sinica

Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI ID:
1560912
Journal Information:
Acta Biochimica et Biophysica Sinica, Journal Name: Acta Biochimica et Biophysica Sinica Vol. 51 Journal Issue: 10; ISSN 1672-9145
Publisher:
China Science Publishing & Media Ltd.Copyright Statement
Country of Publication:
Country unknown/Code not available
Language:
English
Citation Metrics:
Cited by: 50 works
Citation information provided by
Web of Science

References (63)

CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations journal May 2012
Comparative co-expression analysis in plant biology: Comparative transcriptomics in plants journal May 2012
Utility and Limitations of Using Gene Expression Data to Identify Functional Associations journal December 2016
PhytoNet: comparative co-expression network analyses across phytoplankton and land plants journal April 2018
ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa journal January 2014
Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa journal January 2017
Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum ) journal September 2018
A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novel Arabidopsis thaliana abiotic stress genes journal November 2014
Co-expression analysis reveals a group of genes potentially involved in regulation of plant response to iron-deficiency journal January 2015
Physiological Responses and Gene Co-Expression Network of Mycorrhizal Roots under K + Deprivation journal February 2017
A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants journal April 2017
A contribution to the study of plant development evolution based on gene co-expression networks journal January 2013
Elucidating gene function and function evolution through comparison of co-expression networks of plants journal August 2014
PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species journal March 2011
ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking journal June 2013
A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana journal February 2016
Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease journal July 2015
Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize journal November 2018
Development of functional modules based on co-expression patterns for cell-wall biosynthesis related genes in rice journal February 2016
Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules journal March 2017
Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks journal April 2009
Transcriptional regulation of nitrogen-associated metabolism and growth journal October 2018
Gene co-expression network reconstruction: a review on computational methods for inferring functional information from plant-based expression data journal April 2017
Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data journal January 2015
Beyond Genomics: Studying Evolution with Gene Coexpression Networks journal April 2017
Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology journal January 2007
“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks journal March 2012
The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics journal February 2016
Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems journal September 2014
araGWAB: Network-based boosting of genome-wide association studies in Arabidopsis thaliana journal February 2018
RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation journal March 2015
Integrating ChIP-seq with other functional genomics data journal March 2018
Co-expression tools for plant biology: opportunities for hypothesis generation and caveats journal December 2009
Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana journal August 2011
Biclustering on expression data: A review journal October 2015
Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon journal June 2017
Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias journal November 2016
Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane journal January 2016
Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks journal July 2018
Evolution of Daily Gene Co-expression Patterns from Algae to Plants journal July 2017
FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants journal January 2016
GeneMANIA update 2018 journal June 2018
QUBIC: a qualitative biclustering algorithm for analyses of gene expression data journal June 2009
PLANEX: the plant co-expression database journal January 2013
Identification of Transcription Factors Involved in Rice Secondary Cell Wall Formation journal October 2013
Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis journal July 2012
Survey of Genes Involved in Rice Secondary Cell Wall Formation Through a Co-Expression Network journal October 2013
Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells journal November 2017
Large-Scale Co-Expression Approach to Dissect Secondary Cell Wall Formation Across Plant Species journal January 2011
Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data journal September 2015
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis journal March 2015
Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study journal January 2013
Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data journal August 2017
Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice journal May 2011
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species journal October 2014
Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development journal November 2018
Transcriptional Coordination of the Metabolic Network in Arabidopsis journal August 2006
Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry journal July 2018
Comparison of co-expression measures: mutual information, correlation, and model based indices journal January 2012
A comprehensive evaluation of module detection methods for gene expression data journal March 2018
Learning from Co-expression Networks: Possibilities and Challenges journal April 2016
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index journal December 2017
Advantages and limitations of current network inference methods journal August 2010