Gene co-expression network reconstruction: a review on computational methods for inferring functional information from plant-based expression data

Tools of the trade: studying molecular networks in plants

(2016) Sebastian Proost et al.   CURRENT OPINION IN PLANT BIOLOGY

ORA47 (octadecanoid-responsive AP2/ERF-domain transcription factor 47) regulates jasmonic acid and abscisic acid biosynthesis and signaling through binding to a novelcis-element

(2016) Hsing-Yu Chen et al.   NEW PHYTOLOGIST

CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool

(2016) Oren Tzfadia et al.   Frontiers in Plant Science

Learning from Co-expression Networks: Possibilities and Challenges

(2016) Elise A. R. Serin et al.   Frontiers in Plant Science

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

(2015) S. Ballouz et al.   BIOINFORMATICS

Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation

(2015) Patrick T. Ryan et al.   BMC GENOMICS

Identification of crucial genes in intracranial aneurysm based on weighted gene coexpression network analysis

(2015) X Zheng et al.   CANCER GENE THERAPY

Prediction of Gene Co-Expression by Quantifying Heterogeneous Features

(2015) Abbasali Emamjomeh et al.   Current Bioinformatics

Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data

(2015) Zhi-Ping Liu   CURRENT GENOMICS

Transcriptome analysis in Cucumis sativus identifies genes involved in multicellular trichome development

(2015) Jun-Long Zhao et al.   GENOMICS

De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat

(2015) Jinpeng Zhang et al.   GENOMICS

Reconstruction of gene co-expression network from microarray data using local expression patterns

(2014) Swarup Roy et al.   BMC BIOINFORMATICS

Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding

(2014) Arun Kommadath et al.   BMC GENOMICS

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa

(2014) Sergiu Netotea et al.   BMC GENOMICS

ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks

(2014) Ricardo A Chávez Montes et al.   BMC PLANT BIOLOGY

Review on statistical methods for gene network reconstruction using expression data

(2014) Y.X. Rachel Wang et al.   JOURNAL OF THEORETICAL BIOLOGY

SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples

(2014) Hari Krishna Yalamanchili et al.   NUCLEIC ACIDS RESEARCH

GeneFriends: a human RNA-seq-based gene and transcript co-expression database

(2014) Sipko van Dam et al.   NUCLEIC ACIDS RESEARCH

ImmuCo: a database of gene co-expression in immune cells

(2014) Pingzhang Wang et al.   NUCLEIC ACIDS RESEARCH

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems

(2014) Yasunobu Okamura et al.   NUCLEIC ACIDS RESEARCH

Gene Co-Expression Modules as Clinically Relevant Hallmarks of Breast Cancer Diversity

(2014) Denise M. Wolf et al.   PLoS One

Elucidating gene function and function evolution through comparison of co-expression networks of plants

(2014) Bjoern O. Hansen et al.   Frontiers in Plant Science

Construction and validation of a gene co-expression network in grapevine (Vitis vinifera. L.)

(2014) Ying-Hai Liang et al.   Horticulture Research

Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana

(2013) Federico M. Giorgi et al.   BIOINFORMATICS

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)

(2013) Darren CJ Wong et al.   BMC GENOMICS

PLANEX: the plant co-expression database

(2013) Won Yim et al.   BMC PLANT BIOLOGY

Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study

(2013) F Feltus et al.   BMC Systems Biology

Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data

(2013) L. Lopez-Kleine et al.   Briefings in Functional Genomics

Leveraging gene co-expression networks to pinpoint the regulation of complex traits and disease, with a focus on cardiovascular traits

(2013) M. Rotival et al.   Briefings in Functional Genomics

Stress induces remodelling of yeast interaction and co-expression networks

(2013) Sonja Lehtinen et al.   Molecular BioSystems

The arbuscular mycorrhizal symbiosis attenuates symptom severity and reduces virus concentration in tomato infected by Tomato yellow leaf curl Sardinia virus (TYLCSV)

(2013) Giulia Maffei et al.   MYCORRHIZA

Canonical correlation analysis for RNA-seq co-expression networks

(2013) Shengjun Hong et al.   NUCLEIC ACIDS RESEARCH

ATTED-II in 2014: Evaluation of Gene Coexpression in Agriculturally Important Plants

(2013) Takeshi Obayashi et al.   PLANT AND CELL PHYSIOLOGY

Coexpression network analysis associated with call of rice seedlings for encountering heat stress

(2013) Neelam K. Sarkar et al.   PLANT MOLECULAR BIOLOGY

Reconstruction of Cellular Signal Transduction Networks Using Perturbation Assays and Linear Programming

(2013) Bettina Knapp et al.   PLoS One

Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics

(2013) Jie Xiong et al.   Database-The Journal of Biological Databases and Curation

DeGNServer: Deciphering Genome-Scale Gene Networks through High Performance Reverse Engineering Analysis

(2013) Jun Li et al.   Biomed Research International

Utilizing RNA-Seq data for de novo coexpression network inference

(2012) Ovidiu D. Iancu et al.   BIOINFORMATICS

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

(2012) Danielle G Lemay et al.   BMC BIOINFORMATICS

Comparison of co-expression measures: mutual information, correlation, and model based indices

(2012) Lin Song et al.   BMC BIOINFORMATICS

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

(2012) Shan Wang et al.   BMC PLANT BIOLOGY

Towards understanding how molecular networks evolve in plants

(2012) Lee Chae et al.   CURRENT OPINION IN PLANT BIOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations

(2012) Stefanie De Bodt et al.   NEW PHYTOLOGIST

MAGNET: MicroArray Gene expression and Network Evaluation Toolkit

(2012) G. C. Linderman et al.   NUCLEIC ACIDS RESEARCH

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals

(2012) Takeshi Obayashi et al.   NUCLEIC ACIDS RESEARCH

Comparative co-expression analysis in plant biology

(2012) SARA MOVAHEDI et al.   PLANT CELL AND ENVIRONMENT

Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches

(2012) A. Fukushima et al.   PLANT PHYSIOLOGY

Comparing Statistical Methods for Constructing Large Scale Gene Networks

(2012) Jeffrey D. Allen et al.   PLoS One

Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis

(2012) Lida Zhang et al.   PLoS One

RNA-Seq Provides New Insights in the Transcriptome Responses Induced by the Carcinogen Benzo[a]pyrene

(2012) J. van Delft et al.   TOXICOLOGICAL SCIENCES

Coexpression network analysis in chronic hepatitis B and C hepatic lesions reveals distinct patterns of disease progression to hepatocellular carcinoma

(2012) Danning He et al.   Journal of Molecular Cell Biology

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses

(2012) Tahereh Deihimi et al.   SpringerPlus

SNPxGE2: a database for human SNP-coexpression associations

(2011) Y. Wang et al.   BIOINFORMATICS

BiC: a web server for calculating bimodality of coexpression between gene and protein networks

(2011) G. C. Linderman et al.   BIOINFORMATICS

CGCDB: A web-based resource for the investigation of gene coexpression in CHO cell culture

(2011) Colin Clarke et al.   BIOTECHNOLOGY AND BIOENGINEERING

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

(2011) Artem Lysenko et al.   BMC BIOINFORMATICS

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

(2011) Jeff Skinner et al.   BMC BIOINFORMATICS

Metabolic network reconstruction: advances in in silico interpretation of analytical information

(2011) Ning Chen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops

(2011) Keiichi Mochida et al.   PLANT AND CELL PHYSIOLOGY

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants

(2011) T. Obayashi et al.   PLANT AND CELL PHYSIOLOGY

Coexpression-Based Clustering of Arabidopsis Root Genes Predicts Functional Modules in Early Phosphate Deficiency Signaling

(2011) W.-D. Lin et al.   PLANT PHYSIOLOGY

Arabidopsis lysin-motif proteins LYM1 LYM3 CERK1 mediate bacterial peptidoglycan sensing and immunity to bacterial infection

(2011) R. Willmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Tetrahymena Gene Expression Database (TGED): A resource of microarray data and co-expression analyses for Tetrahymena

(2011) Jie Xiong et al.   Science China-Life Sciences

DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data

(2010) Bao-Hong Liu et al.   BIOINFORMATICS

CoP: a database for characterizing co-expressed gene modules with biological information in plants

(2010) Y. Ogata et al.   BIOINFORMATICS

Fast and efficient dynamic nested effects models

(2010) Holger Fröhlich et al.   BIOINFORMATICS

Interactional and functional centrality in transcriptional co-expression networks

(2010) Edi Prifti et al.   BIOINFORMATICS

geWorkbench: an open source platform for integrative genomics

(2010) Aris Floratos et al.   BIOINFORMATICS

A general co-expression network-based approach to gene expression analysis: comparison and applications

(2010) Jianhua Ruan et al.   BMC Systems Biology

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

COXPRESdb: a database to compare gene coexpression in seven model animals

(2010) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

(2010) Kazuki Hamada et al.   PLANT AND CELL PHYSIOLOGY

Identifying functional modules using expression profiles and confidence-scored protein interactions

(2009) Igor Ulitsky et al.   BIOINFORMATICS

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data

(2009) Daniel Jupiter et al.   BMC BIOINFORMATICS

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus

(2009) Valentina Fiorilli et al.   NEW PHYTOLOGIST

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice

(2009) T.-H. Lee et al.   PLANT PHYSIOLOGY

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

(2008) Antonio Reverter et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Regulon organization of Arabidopsis

(2008) Wieslawa I Mentzen et al.   BMC PLANT BIOLOGY

GeneCAT—novel webtools that combine BLAST and co-expression analyses

(2008) Marek Mutwil et al.   NUCLEIC ACIDS RESEARCH

ATTED-II provides coexpressed gene networks for Arabidopsis

(2008) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense

(2008) K.-C. Kim et al.   PLANT CELL

CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis

(2008) V. Srinivasasainagendra et al.   PLANT PHYSIOLOGY