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

Journal Article · · Acta Biochimica et Biophysica Sinica

Not Available

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 Journal Issue: 10 Vol. 51; ISSN 1672-9145
Publisher:
China Science Publishing & Media Ltd.Copyright Statement
Country of Publication:
Country unknown/Code not available
Language:
English

References (63)

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A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana journal February 2016
Physiological Responses and Gene Co-Expression Network of Mycorrhizal Roots under K + Deprivation journal February 2017
Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data journal August 2017
Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry journal July 2018
PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species journal March 2011
RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation journal March 2015
A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants journal April 2017
Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize journal November 2018
Co-expression tools for plant biology: opportunities for hypothesis generation and caveats journal December 2009
Comparative co-expression analysis in plant biology: Comparative transcriptomics in plants journal May 2012
CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations journal May 2012
Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon journal June 2017
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
Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum ) journal September 2018
Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules journal March 2017
Comparison of co-expression measures: mutual information, correlation, and model based indices journal January 2012
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Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study journal January 2013
Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias journal November 2016
Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease journal July 2015
Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells journal November 2017
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“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks journal March 2012
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The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics journal February 2016
Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis journal March 2015
Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data journal January 2015
Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems journal September 2014
Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development journal November 2018
Large-Scale Co-Expression Approach to Dissect Secondary Cell Wall Formation Across Plant Species journal January 2011
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
Learning from Co-expression Networks: Possibilities and Challenges journal April 2016
Evolution of Daily Gene Co-expression Patterns from Algae to Plants journal July 2017

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