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Gene co-expression detection software tools | Gene expression data analysis

Ever since the publication of the first gene expression arrays, the correlated expression of genes involved in a related molecular process has been used to predict functional relations between gene pairs (Chu et al., 1998). Large amounts of…
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SEEK
Web

SEEK Search-Based Exploration of Expression Compendium

A computational gene co-expression search engine. SEEK provides biologists with…

A computational gene co-expression search engine. SEEK provides biologists with a way to navigate the massive human expression compendium that now contains thousands of expression datasets. SEEK…

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geneRecommender
Desktop

geneRecommender

Allows to identify genes that are coexpressed with a given set of genes of…

Allows to identify genes that are coexpressed with a given set of genes of interest. geneRecommender takes a query list of genes, finds experiments in which those genes appear to be coregulated, and…

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GeneMANIA
Web

GeneMANIA

Finds other genes that are related to a set of input genes, using a very large…

Finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression,…

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VCNet
Desktop

VCNet

Constructs gene co-expression network (GCN) from RNA-seq data. VCNet performs a…

Constructs gene co-expression network (GCN) from RNA-seq data. VCNet performs a statistical hypothesis test based on the correlation matrix of a gene-gene pair using the Frobenius norm. It can detect…

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LEAP
Desktop

LEAP Lag-based Expression Association for Pseudotime-series

Utilizes the estimated pseudotime of the cells to find gene co-expression that…

Utilizes the estimated pseudotime of the cells to find gene co-expression that involves time delay. LEAP sorts cells according to the estimated pseudotime and then computes the maximum correlation of…

CORNET
Web

CORNET

A user-friendly tool for data mining and integration in Arabidopsis. CORNET…

A user-friendly tool for data mining and integration in Arabidopsis. CORNET allows the browsing of microarray data, the construction of coexpression and protein-protein interaction (PPI) networks and…

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WeGET
Web

WeGET Weighted Gene Expression Tool and database

A computational tool to find mammalian genes that strongly co-express with a…

A computational tool to find mammalian genes that strongly co-express with a human query gene set of interest. Currently, WeGET uses over one thousand human and murine microarray data sets in its…

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propr
Desktop

propr

Provides a fast implementation of two measures of proportionality previously…

Provides a fast implementation of two measures of proportionality previously shown to rectify the issue of spurious correlation in the setting of compositional data. Propr offers a valid alternative…

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CODfinder
Desktop

CODfinder

Determines co-expression domains (CODs). CODfinder is based on methods used to…

Determines co-expression domains (CODs). CODfinder is based on methods used to identify topologically associating domains (TADs). It computes an average co-expression signal between upstream and…

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GEM2Net
Web

GEM2Net

A module of CATdb to mine co-expression units and decipher Arabidopsis gene…

A module of CATdb to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a…

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dhga
Desktop

dhga Differential Hub Gene Analysis

Permits to group genes in the Gene Co-expression Network (GCN) into various…

Permits to group genes in the Gene Co-expression Network (GCN) into various categories. dhga is based on the gene connectivity. It allows to identify hub genes in a gene co-expression network from…

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Gene2Net
Dataset

Gene2Net

Allows users to expand one or multiple genes into a small network. Gene2Net…

Allows users to expand one or multiple genes into a small network. Gene2Net performs guilt-by-association (GBA) analysis based on the three protein co-expression networks generated from the study of…

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DECODE
Desktop

DECODE Differential Co-expression and Differential Expression

An analytical approach to integrate differential co-expression (DC) and…

An analytical approach to integrate differential co-expression (DC) and differential expression (DE) analyses of gene expression data. DECODE allows one to study the combined features of DC and DE of…

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km2gcn
Desktop

km2gcn k-means to gene co-expression network

Allows users to generate gene co-expression network (GCN). km2gcn improves the…

Allows users to generate gene co-expression network (GCN). km2gcn improves the partitions generated from gene co-expression networks. This tool tries to reach the desired value for misplaced genes.…

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RLowPC
Desktop

RLowPC Relevance Low order Partial Correlation

Reduces the search space by only picking the top ranked genes from partial…

Reduces the search space by only picking the top ranked genes from partial correlation analysis. RLowPC computes the Partial Correlation (PC) by removing the linear dependencies from the shared…

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CORTx
Web

CORTx

Provides numerous additional ways to visualize and explore the dataset…

Provides numerous additional ways to visualize and explore the dataset initially described in "A Transcriptomic Atlas of Mouse Neocortical Layers". CORTx is a web interface that finds…

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CoExpNetViz
Web
Desktop

CoExpNetViz comparative Co-Expression Network construction and Visualization

A computational tool that uses a set of query or "bait" genes as an…

A computational tool that uses a set of query or "bait" genes as an input (chosen by the user) and a minimum of one pre-processed gene expression dataset. The CoExpNetViz algorithm proceeds…

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AraSTressRegNet
Web

AraSTressRegNet

A powerful computational approach for selecting candidate genes for screening…

A powerful computational approach for selecting candidate genes for screening insertion mutants. We combined ranking of Arabidopsis thaliana regulatory genes according to their expression in response…

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RECoN
Web

RECoN Rice Environment Coexpression Network

Allows users to obtain tightly coexpressed groups of genes that revealed the…

Allows users to obtain tightly coexpressed groups of genes that revealed the modular organization of genes. RECoN is able to explore coexpression clusters within their stress transcriptome and…

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EnsembleNet
Dataset

EnsembleNet

Provides an easy access to Neighbor Counting Ensemble (NCE) predictions with…

Provides an easy access to Neighbor Counting Ensemble (NCE) predictions with the aim to facilitate hypothesis generation. EnsembleNet provides three approaches to retrieve functional information of…

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CLIC
Web
Desktop

CLIC Clustering by Inferred Co-expression

Allows to expand biological pathways based on co-expression. CLIC harnesses a…

Allows to expand biological pathways based on co-expression. CLIC harnesses a compendium of gene expression datasets to partition an input gene set into disjoint co-expression modules (CEMs),…

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RapaNet
Dataset

RapaNet

Helps to identify gene relationships and analyze gene functions. RapaNet was…

Helps to identify gene relationships and analyze gene functions. RapaNet was constructed using 143 Brassica microarrays based on the Brassica rapa 300k Microarray v2.0. The database allows to search…

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SWIM
Desktop

SWIM SWItch Miner

Identifies switch genes in several human cancers. SWIM is a wizard-like…

Identifies switch genes in several human cancers. SWIM is a wizard-like software implementation of a procedure designed to extract information from complex networks. The software is amenable to…

iSyTE
Web

iSyTE integrated Systems Tool for Eye gene discovery

Permits prioritization of candidate genes associated with human congenital…

Permits prioritization of candidate genes associated with human congenital cataract. iSyTE was created using an in silico subtraction approach by which lens microarray data sets are compared to a…

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petal
Desktop

petal

A tool for generating co-expression network models of whole-genomics…

A tool for generating co-expression network models of whole-genomics experiments. petal is very user-friendly by requiring little prior knowledge of network science without sacrificing the quality…

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GeneCAT
Web

GeneCAT Gene Co-expression Analysis Toolbox

Introduces several novel microarray data analyzing tools. GeneCAT provides the…

Introduces several novel microarray data analyzing tools. GeneCAT provides the user with both standard co-expression tools, such as gene clustering and expression profiling, and also includes tools…

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HO GSVD
Desktop

HO GSVD

Provides a sequence-independent comparative framework for two or more genomic…

Provides a sequence-independent comparative framework for two or more genomic datasets, where the variables and operations represent biological reality. The approximately common HO GSVD subspace…

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GSNCA
Desktop

GSNCA Gene Sets Net Correlations Analysis

Provides a multivariate differential coexpression test that accounts for the…

Provides a multivariate differential coexpression test that accounts for the complete correlation structure between genes. GSNCA characterizes differences in coexpression networks, without requiring…

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PlaNet
Web

PlaNet Plant Network

A platform of web-tools dedicated to visualization and analysis of plant…

A platform of web-tools dedicated to visualization and analysis of plant co-function networks. PlaNet integrates genomics, transcriptomics, phenomics, and ontology analyses across seven plant species…

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CoXpress
Desktop

CoXpress

Allows researchers to identify groups of genes that are differentially…

Allows researchers to identify groups of genes that are differentially co-expressed. CoXpress uses a re-sampling method to calculate a p-value for each group, and provides several methods for the…

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WGCNA
Desktop

WGCNA WeiGhted Correlation Network Analysis

A comprehensive collection of R functions for performing various aspects of…

A comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. WGCNA includes functions for network construction, module detection, gene selection,…

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G-NEST
Desktop

G-NEST Gene NEighborhood Scoring Tool

Scores the evolutionary conservation of gene neighborhoods using syntenic…

Scores the evolutionary conservation of gene neighborhoods using syntenic blocks. G-NEST combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene…

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FNTM
Web

FNTM Functional Networks of Tissues in Mouse

Provides biomedical researchers with tissue-specific predictions of functional…

Provides biomedical researchers with tissue-specific predictions of functional relationships between proteins in the most widely used model organism for human disease, the laboratory mouse. Users can…

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ComPlEx
Web

ComPlEx Comparative analysis of Plant co-Expression networks

A comprehensive analysis of gene regulation evolution in plants and built a web…

A comprehensive analysis of gene regulation evolution in plants and built a web tool for comparative analysis of plant co-expression networks. ComPlEx visualizes conserved link in co-expression…

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ATCOECIS
Web

ATCOECIS

Identifies coexpressed genes or gene coexpression neighborhoods associated with…

Identifies coexpressed genes or gene coexpression neighborhoods associated with cis-regulatory motifs or Gene Ontology (GO) categories. ATCOECIS allows (1) to analyze the properties and the…

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CressExpress
Web

CressExpress

A user-friendly, online, coexpression analysis tool for Arabidopsis…

A user-friendly, online, coexpression analysis tool for Arabidopsis (Arabidopsis thaliana) microarray expression data that computes patterns of correlated expression between user-entered query genes…

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Coexnet
Desktop

Coexnet CO-EXpression NETworks

Determines the gene expression matrix from Gene Expression Omnibus (GEO)…

Determines the gene expression matrix from Gene Expression Omnibus (GEO) DataSets. Coexnet uses two different methods in order to make the normalization process. It is able to pass from multi-probe…

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DiffCoEx
Desktop

DiffCoEx

Identifies gene coexpression differences between multiple conditions. DiffCoEx…

Identifies gene coexpression differences between multiple conditions. DiffCoEx is a method for identifying correlation pattern changes, which builds on the commonly used Weighted Gene Coexpression…

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REMOCOD
Web

REMOCOD REgulatory MOtif COmbination Detector

Identifies pairs of transcription factor binding sites (TFBSs) in sequences of…

Identifies pairs of transcription factor binding sites (TFBSs) in sequences of a set of co-regulated genes thanks to gene IDs. REMOCOD provides a web interface which detects over-represented TFBSs in…

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CEMiTool
Desktop

CEMiTool Co-expression Modules Identification Tool

Optimizes weighted gene co-expression network analysis (WGCNA) gene…

Optimizes weighted gene co-expression network analysis (WGCNA) gene co-expression module discovery. CEMiTool permits users to specify network parameters to improve the finding. Thank to discovered…

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HGCA
Web

HGCA Human Gene Correlation Analysis

A tool to classify human genes according to their coexpression levels and to…

A tool to classify human genes according to their coexpression levels and to identify overrepresented annotation terms in correlated gene groups. HGCA is based on the Pearson Correlation Coefficient…

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CluGene
Desktop

CluGene

Permits the identification of coregulated, co-localized and co-expressed genes.…

Permits the identification of coregulated, co-localized and co-expressed genes. CluGene integrates gene expression analysis profiling with automated search and identification of co-expressed and…

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STARNET
Web

STARNET

A web-based tool that allows post hoc visual analysis of correlations that are…

A web-based tool that allows post hoc visual analysis of correlations that are derived from expression microarray data. STARNET facilitates user discovery of putative gene regulatory networks in a…

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