Gene set analysis (GSA) software tools | Gene expression data analysis
Gene set analysis (GSA) incorporates biological information into statistical knowledge to identify gene sets differently expressed between two or more phenotypes. It allows us to gain an insight into the functional working mechanism of cells beyond the detection of differently…
Web app
A A A Enrichr Enrichr

Enrichr

An integrative web-based and mobile software application that includes new…

An integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to…

Web app
A A A g:Profiler g:Profiler

g:Profiler

A popular collection of web tools for functional analysis. g:GOSt and g:Cocoa…

A popular collection of web tools for functional analysis. g:GOSt and g:Cocoa combine comprehensive methods for interpreting gene lists, ordered lists and list collections in the context of…

Desktop app
Web app
Babelomics Babelomics

Babelomics

A web application for the functional analysis of gene expression and genomic…

A web application for the functional analysis of gene expression and genomic data. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a…

Web app
A A A GeneCruiser GeneCruiser

GeneCruiser

Provides integrated access to genomic information freely available from public…

Provides integrated access to genomic information freely available from public data sources. It relies on a regularly updated database that retrieves and indexes the mappings between microarray…

A A A YunBe YunBe

YunBe

A gene set analysis algorithm for biomarker identification in the cloud. YunBe…

A gene set analysis algorithm for biomarker identification in the cloud. YunBe is open-source and freely accessible within the Amazon Elastic MapReduce service.

Web app
A A A Genome Expression… Genome Expression Pathway Analysis Tool

GEPAT Genome Expression Pathway Analysis Tool

A web-based tool offering an integrated analysis of transcriptome data under…

A web-based tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. GEPAT imports various formats of oligonucleotide arrays, cDNA arrays and data…

Desktop app
A A A ArrayPlex ArrayPlex

ArrayPlex

A software package that centrally provides a large number of flexible toolsets…

A software package that centrally provides a large number of flexible toolsets useful for functional genomics, including microarray data storage, quality assessments, data visualization, gene…

A A A clipper clipper

clipper

Implements topological gene set analysis using a two-step empirical approach.…

Implements topological gene set analysis using a two-step empirical approach. clipper exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In…

Desktop app
A A A GeneAnswers GeneAnswers

GeneAnswers

Provides an integrated solution for a group of genes and specified categories…

Provides an integrated solution for a group of genes and specified categories (biological or medical functions, such as Gene Ontology, Disease Ontology, KEGG, etc) to reveal the potential…

Web app
A A A GeneAnalytics GeneAnalytics

GeneAnalytics

A comprehensive and easy-to-apply gene set analysis tool for rapid…

A comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next…

Desktop app
A A A RNAModR RNAModR

RNAModR

A package to analyse and visualise the transcriptome-wide distribution of mRNA…

A package to analyse and visualise the transcriptome-wide distribution of mRNA modifications. RNAModR provides functions to map lists of genomic loci of RNA modifications to a reference mRNA…

Desktop app
A A A Network Enrichment… Network Enrichment Analysis Test

NEAT Network Enrichment Analysis Test

A test for network enrichment analysis that aims to overcome some limitations…

A test for network enrichment analysis that aims to overcome some limitations of existing resampling-based tests. The main idea behind NEAT is that, under the null hypothesis of no enrichment, the…

Desktop app
A A A rapid Gene Set… rapid Gene Set Enrichment Analysis

rapidGSEA rapid Gene Set Enrichment Analysis

A suite to facilitate permutation-based gene set enrichment analysis and for…

A suite to facilitate permutation-based gene set enrichment analysis and for commonly available multi-core CPUs and CUDA-enabled GPUs. rapidGSEA integrates two tools: udaGSEA is a CUDA-accelerated…

Web app
A A A Model Organisms… Model Organisms Projected on a Human Integrated…

MORPHIN Model Organisms Projected on a Human Integrated Gene Network

A web-based discovery tool for human disease studies. MORPHIN investigates…

A web-based discovery tool for human disease studies. MORPHIN investigates human diseases by an orthology-based projection of a set of model organism genes onto a genome-scale human gene network.…

Desktop app
A A A TopKLists TopKLists

TopKLists

Allows for statistical inference on the lengths of informative (top-k) partial…

Allows for statistical inference on the lengths of informative (top-k) partial lists, for stochastic aggregation of full or partial lists, and for graphical exploration of the input and consolidated…

Web app
A A A Constellation Map Constellation Map

Constellation Map

A tool to visualize and interpret the results when enrichment analyses yield a…

A tool to visualize and interpret the results when enrichment analyses yield a long list of significantly enriched gene sets. Constellation Map identifies commonalities that explain the enrichment of…

Desktop app
A A A Ensemble of Gene Set… Ensemble of Gene Set Enrichment Analyses

EGSEA Ensemble of Gene Set Enrichment Analyses

A package which implements the Ensemble of Gene Set Enrichment Analysis (EGSEA)…

A package which implements the Ensemble of Gene Set Enrichment Analysis (EGSEA) algorithm that utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate…

Desktop app
A A A ABAEnrichment ABAEnrichment

ABAEnrichment

An R package that tests for expression enrichment in specific brain regions at…

An R package that tests for expression enrichment in specific brain regions at different developmental stages using expression information gathered from multiple regions of the adult and developing…

Desktop app
Spatial Analysis of… Spatial Analysis of Network Associations

SANTA Spatial Analysis of Network Associations

A package which provides methods for measuring the strength of association…

A package which provides methods for measuring the strength of association between a network and a phenotype. SANTA quantifies the strength of association between a gene set and a network, and…

Desktop app
A A A GSA-Lightning GSA-Lightning

GSA-Lightning

A fast implementation of permutation-based gene set analysis. GSA-Lightning is…

A fast implementation of permutation-based gene set analysis. GSA-Lightning is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is…

Desktop app
A A A GiANT GiANT

GiANT

An approach for assessing uncertainty in the definition of gene sets. This is…

An approach for assessing uncertainty in the definition of gene sets. This is an essential step when new gene sets are constructed from domain knowledge or given gene sets are suspected to be…

Desktop app
A A A Gene Set Clustering… Gene Set Clustering based on Functional annotation

GeneSCF Gene Set Clustering based on Functional annotation

Predicts the functionally relevant biological information for a set of genes in…

Predicts the functionally relevant biological information for a set of genes in a real-time updated manner. GeneSCF is designed to handle information from more than 4000 organisms from freely…

Desktop app
A A A Gene Set Variation… Gene Set Variation Analysis

GSVA Gene Set Variation Analysis

A gene set enrichment (GSE) method that estimates variation of pathway activity…

A gene set enrichment (GSE) method that estimates variation of pathway activity over a sample population in an unsupervised manner. GSVA provides increased power to detect subtle pathway activity…

Desktop app
A A A Gene Set Enrichment… Gene Set Enrichment Analysis

GSEA Gene Set Enrichment Analysis

A computational method that determines whether an a priori defined set of genes…

A computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA derives…

Web app
A A A GeneWeaver GeneWeaver

GeneWeaver

Combines cross-species data and gene entity integration, scalable hierarchical…

Combines cross-species data and gene entity integration, scalable hierarchical analysis of user data with a community-built and curated data archive of gene sets and gene networks, and tools for data…

Web app
A A A Plant GeneSet… Plant GeneSet Enrichment Analysis toolkit

PlantGSEA Plant GeneSet Enrichment Analysis toolkit

An online websever for gene set enrichment analysis of plant organisms. The…

An online websever for gene set enrichment analysis of plant organisms. The PlantGSEA was designed to serve researchers from plant community with a user-friendly interface as well as…

Web app
A A A NetVenn NetVenn

NetVenn

A network-based web platform for the comparison and analysis of gene lists by…

A network-based web platform for the comparison and analysis of gene lists by combining Venn diagram and gene set enrichment. The tool can integrate gene sets with differentially expressed gene on…

Web app
A A A GeneCodis GeneCodis

GeneCodis

A web-based tool for the ontological analysis of large lists of genes. It can…

A web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of…

Desktop app
A A A MUlti-list SElection… MUlti-list SElection Algorithm

MULSEA MUlti-list SElection Algorithm

Seeks to identify combinatorial regulation by multi-factor effectors,…

Seeks to identify combinatorial regulation by multi-factor effectors, consisting of the following components. MULSEA starts with a pivot ranked list and a collection of other ranked lists over the…

Desktop app
A A A XGSA XGSA

XGSA

A straightforward statistical approach that explicitly takes the cross-species…

A straightforward statistical approach that explicitly takes the cross-species homology mapping into consideration when doing gene set analysis. Simulation experiments confirm that XGSA can avoid…

A A A Pathways, Annotated… Pathways, Annotated list, and Gene-sets…

PAGER Pathways, Annotated list, and Gene-sets Electronic Repository

A database framework to perform integrative “gene-set, network, and pathway…

A database framework to perform integrative “gene-set, network, and pathway analysis”. The PAGER database currently compiles 44 313 genes from 5 species including human, 38 663 PAGs, 324 830…

Desktop app
A A A Adaptive Signature… Adaptive Signature Selection and InteGratioN

ASSIGN Adaptive Signature Selection and InteGratioN

A pathway profiling toolkit which enables robust and context-specific pathway…

A pathway profiling toolkit which enables robust and context-specific pathway analyses by efficiently capturing pathway activity in heterogeneous sets of samples and across profiling technologies.…

Web app
A A A Tribe Tribe

Tribe

Provides a means for researchers to perform reproducible gene set based…

Provides a means for researchers to perform reproducible gene set based analyses seamlessly across webservers and command line tools. Tribe allows users to create analysis pipelines that use their…

Web app
A A A PathwAX PathwAX

PathwAX

A webservice for pathway annotation based on crosstalk derived through FunCoup,…

A webservice for pathway annotation based on crosstalk derived through FunCoup, a framework for genome wide functional association networks. PathwAX runs the BinoX algorithm, which employs…

A A A TargetMine TargetMine

TargetMine

An integrated data warehouse based on the versatile InterMine framework, which…

An integrated data warehouse based on the versatile InterMine framework, which models biological entities (such as genes and proteins) as ‘objects’ and their relationships as ‘references’ to…

Web app
A A A WhichGenes WhichGenes

WhichGenes

An on-line, database-free, web-based tool for easily gathering, building,…

An on-line, database-free, web-based tool for easily gathering, building, storing and exporting always updated gene sets coming from multiple data sources. It allows researchers to elaborate custom…

Desktop app
A A A BubbleGUM BubbleGUM

BubbleGUM

A computational tool that allows to automatically extract phenotype signatures…

A computational tool that allows to automatically extract phenotype signatures based on transcriptomic data and to perform easily multiple GSEA runs in a row. The result is displayed at the global…

Web app
A A A WormExp WormExp

WormExp

A web-based application for a taxon-specific gene set exploration and…

A web-based application for a taxon-specific gene set exploration and enrichment analysis, which is expected to yield novel functional insights into newly determined gene sets. WormExp is based on…

Web app
A A A AtCAST AtCAST

AtCAST

A web-based tool to analyze the relationship between experimental conditions…

A web-based tool to analyze the relationship between experimental conditions among transcriptome data. Users can analyze 'user's transcriptome data' of a new mutant or a new chemical…

Desktop app
A A A stringgaussnet stringgaussnet

stringgaussnet

Allows inferring gene networks starting from a list of differentially expressed…

Allows inferring gene networks starting from a list of differentially expressed (DE) genes by integrating knowledge-based and co-expression network with ease and flexibility. Stringgaussnet allows…

Web app
A A A Reflective Diffusion… Reflective Diffusion and Local Extension

RIDDLE Reflective Diffusion and Local Extension

Uses well developed guilt-by-association principles upon a human gene network…

Uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. RIDDLE is particularly adept at characterizing sets with no annotations, a major…

Desktop app
A A A RDAVIDWebService RDAVIDWebService

RDAVIDWebService

Provides a class-based interface from R programs/scripts to fully…

Provides a class-based interface from R programs/scripts to fully access/control the database for annotation, visualization and integrated discovery, without the need for human interaction on its Web…

Desktop app
A A A Significance Analysis… Significance Analysis of Microarray for Gene Sets

SAM-GS Significance Analysis of Microarray for Gene Sets

Gene set enrichment analysis is subject to some serious problems as a method…

Gene set enrichment analysis is subject to some serious problems as a method for gene-set analysis, potentially leading to unnecessarily high false-positive and false-negative discovery rates.…

Desktop app
A A A Generalized QuSAGE Generalized QuSAGE

Q-Gen Generalized QuSAGE

An extension to the gene set analysis method of QuSAGE. Q-Gen allows for linear…

An extension to the gene set analysis method of QuSAGE. Q-Gen allows for linear mixed models to be applied appropriately within a gene set analysis framework. It provides GSA an added layer of…

Desktop app
A A A Quantitative Set… Quantitative Set Analysis for Gene Expression

QuSAGE Quantitative Set Analysis for Gene Expression

A computational framework for quantitative set analysis of gene expression.…

A computational framework for quantitative set analysis of gene expression. QuSAGE accounts for inter-gene correlations, improves the estimation of the variance inflation factor and, rather than…

Web app
A A A Plant Ontology… Plant Ontology Enrichment Analysis Server

POEAS Plant Ontology Enrichment Analysis Server

A public web server for automated phenomic enrichment analyses of the genes of…

A public web server for automated phenomic enrichment analyses of the genes of A. thaliana. POEAS uses a simple list of genes/proteins as input and perform enrichment analysis and provide results and…

Web app
A A A GEO2Enrichr GEO2Enrichr

GEO2Enrichr

A web application and two browser extensions (one for Chrome and another for…

A web application and two browser extensions (one for Chrome and another for Firefox) designed to ease the extraction of signatures from studies posted on the Gene Expression Omnibus (GEO) database.…

Desktop app
A A A npGSEA npGSEA

npGSEA

Agene set enrichment analysis that is computationally inexpensive, and avoids…

Agene set enrichment analysis that is computationally inexpensive, and avoids the resampling granularity issue. npGSEA allows approximate testing to be done orders of magnitude faster than one could…

Web app
A A A Profiling of complex… Profiling of complex functionality

ProfCom Profiling of complex functionality

A web-based tool for the interpretation of genes that were identified to be…

A web-based tool for the interpretation of genes that were identified to be functionally linked by experiment. ProfCom automatically generates statistically valid hypotheses/biological models from…

Desktop app
A A A integrative Pathway… integrative Pathway Enrichment Analysis Platform

iPEAP integrative Pathway Enrichment Analysis Platform

Handles transcriptomics, proteomics, metabolomics and GWAS data under a unified…

Handles transcriptomics, proteomics, metabolomics and GWAS data under a unified aggregation schema. iPEAP emphasizes on the ability to aggregate various pathway enrichment results generated in…

Desktop app
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A A A Kiwi Kiwi

Kiwi

Processes output data from gene-set analysis and integrates them with a network…

Processes output data from gene-set analysis and integrates them with a network structure such that the inherent connectivity between gene-sets, i.e. not simply the gene overlap, becomes apparent.…

Desktop app
dslice dslice

dslice

Many statistical problems in bioinformatics and genetics can be formulated as…

Many statistical problems in bioinformatics and genetics can be formulated as the testing of associations between a categorical variable and a continuous variable. dslice is an R package to…

Web app
A A A RuleGO RuleGO

RuleGO

A web-based application for describing gene groups using logical rules based on…

A web-based application for describing gene groups using logical rules based on Gene Ontology terms. RuleGO takes as an input two lists of genes: a list of genes to be described and a reference list…

Web app
A A A KEGG Mapper KEGG Mapper

KEGG Mapper

Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and…

Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multiple…

Web app
A A A PathExpand PathExpand

PathExpand

A web-application extending pre-defined protein sets representing cellular…

A web-application extending pre-defined protein sets representing cellular processes by mapping them onto an interaction network and expanding them to include densely interconnected interaction…

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A A A Drosophila Phenotype… Drosophila Phenotype Enrichment Analysis

DroPhEA Drosophila Phenotype Enrichment Analysis

A core module of a web application that facilitates research in insect…

A core module of a web application that facilitates research in insect functional genomics through enrichment analysis on mutant phenotypes of fruit fly (Drosophila melanogaster). The phenotypes…

Web app
A A A Mammalian Phenotype… Mammalian Phenotype Enrichment Analysis

MamPhEA Mammalian Phenotype Enrichment Analysis

A web application dedicated to understanding functional properties of mammalian…

A web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes. MamPhEA allows users to conduct enrichment analysis on predefined or…

Web app
A A A FungiFun FungiFun

FungiFun

A user-friendly web tool for functional enrichment analysis of fungal genes and…

A user-friendly web tool for functional enrichment analysis of fungal genes and proteins. FungiFun offers a modern web interface and creates interactive tables, charts and figures, which users can…

Web app
A A A RAMONA RAMONA

RAMONA

It offers an easy-to-use interface for the simultaneous gene set analysis of…

It offers an easy-to-use interface for the simultaneous gene set analysis of combined omics datasets and is an extension of the previously introduced MONA approach.

Web app
A A A EnrichNet EnrichNet

EnrichNet

A web-service to map gene sets onto a human protein-protein interaction network…

A web-service to map gene sets onto a human protein-protein interaction network and analyze their network associations with mapped cellular pathways, processes and complexes.

Desktop app
A A A NetPathMiner NetPathMiner

NetPathMiner

A general framework for mining, from genome-scale networks, paths that are…

A general framework for mining, from genome-scale networks, paths that are related to specific experimental conditions.

Web app
A A A Lynx Lynx

Lynx

A web-based database and a knowledge extraction engine. Lynx supports…

A web-based database and a knowledge extraction engine. Lynx supports annotation and analysis of high-throughput experimental data and generation of weighted hypotheses regarding genes and molecular…

Web app
A A A REGNET REGNET

REGNET

An integrative platform that maps a myriad of regulation patterns…

An integrative platform that maps a myriad of regulation patterns (transcription and post transcription) to specific biological processes under specific cellular environments.

Desktop app
A A A ErmineJ ErmineJ

ErmineJ

Performs analyses of gene sets in high-throughput genomics data such as gene…

Performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. A typical goal is to determine whether particular biological pathways are "doing…

Web app
A A A Functional… Functional Specification

FunSpec Functional Specification

Inputs a list of yeast gene names, and outputs a summary of functional classes,…

Inputs a list of yeast gene names, and outputs a summary of functional classes, cellular localizations, protein complexes, etc. that are enriched in the list.

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A A A GO2MSIG GO2MSIG

GO2MSIG

Enables the bioinformatician and non-bioinformatician alike to generate gene…

Enables the bioinformatician and non-bioinformatician alike to generate gene sets required for GSEA analysis for almost any organism for which GO term association data exists.

Desktop app
A A A Enrichment Map Enrichment Map

Enrichment Map

Allows you to visualize the results of gene-set enrichment as a network. It…

Allows you to visualize the results of gene-set enrichment as a network. It will operate on any generic enrichment results as well as specifically on Gene Set Enrichment Analysis (GSEA) results.…

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G T A T C G C T A ChIP-Enrich ChIP-Enrich

ChIP-Enrich

Tests ChIP-seq peak data for enrichment of biological pathways, Gene Ontology…

Tests ChIP-seq peak data for enrichment of biological pathways, Gene Ontology terms, and other types of gene sets. Using an input .BED file, ChIP-Enrich assigns peaks to genes based on a chosen…

Web app
A A A Connections between… Connections between Diseases and Developmental…

Connections between Diseases and Developmental Gene Sets

An approach that identifies significant overlap of gene sets with groups of…

An approach that identifies significant overlap of gene sets with groups of related diseases in a hierarchical disease taxonomy.

Web app
A A A ConceptGen ConceptGen

ConceptGen

A web-based gene set enrichment and gene set relation mapping tool that is…

A web-based gene set enrichment and gene set relation mapping tool that is streamlined and simple to use.

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A A A LRpath LRpath

LRpath

Performs gene set enrichment testing, an approach used to test for predefined…

Performs gene set enrichment testing, an approach used to test for predefined biologically-relevant gene sets that contain more significant genes from an experimental dataset than expected by chance.…

Web app
A A A R spider R spider

R spider

Implements the Global Network statistical framework to analyze gene list using…

Implements the Global Network statistical framework to analyze gene list using as reference knowledge a global gene network constructed by combining signaling and metabolic pathways from Reactome and…

Web app
A A A Genes2Networks Genes2Networks

Genes2Networks

A web-based software that can help experimental biologists to interpret lists…

A web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of…

Web app
A A A GeneSetDB GeneSetDB

GeneSetDB

A comprehensive meta-database with associated gene set enrichment analysis…

A comprehensive meta-database with associated gene set enrichment analysis statistical tools, which integrates a large number of other biological databases for gene set analysis.

Web app
GenCLiP GenCLiP

GenCLiP

A web-based text-mining server which can analyze human genes with enriched…

A web-based text-mining server which can analyze human genes with enriched keywords and molecular interactions. GenCLiP 2.0 offers two unique features: i) analysis of gene functions with free terms…

Desktop app
A A A Evaluation of… Evaluation of Dependency Differentiality

EDDY Evaluation of Dependency Differentiality

A statistical test for the differential dependency relationship of a set of…

A statistical test for the differential dependency relationship of a set of genes between two given conditions. For each condition, possible dependency network structures are enumerated and their…

Web app
A A A Gitools Gitools

Gitools

A framework for analysis and visualization of multidimensional genomic data…

A framework for analysis and visualization of multidimensional genomic data using interactive heat-maps.

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A A A Integrative… Integrative Multi-species Prediction

IMP Integrative Multi-species Prediction

An interactive web server that enables molecular biologists to interpret…

An interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions…

Web app
A A A GeneMANIA GeneMANIA

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,…

Desktop app
A A A JEPETTO JEPETTO

JEPETTO

Performs integrated gene set analysis using information from interaction,…

Performs integrated gene set analysis using information from interaction, pathways and processes databases. JEPETTO uses the TopoGSA server to identify topological analogies between the user selected…

Web app
A A A ADGO ADGO

ADGO

Provides composite interpretations for microarray data comparing two sample…

Provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. Some other tools also incorporate…

Web app
A A A GeneTrail GeneTrail

GeneTrail

A web service allowing the integrated analysis of transcriptomic, miRNomic,…

A web service allowing the integrated analysis of transcriptomic, miRNomic, genomic, and proteomic datasets. GeneTrail offers multiple statistical tests, a large number of predefined reference sets,…

Web app
A A A gsGator gsGator

gsGator

A web-based platform for functional interpretation of gene sets with useful…

A web-based platform for functional interpretation of gene sets with useful features such as cross-species GSA, simultaneous analysis of multiple gene sets, and a fully integrated network viewer.

Web app
A A A PhenoFam PhenoFam

PhenoFam

A web-based application that performs gene set enrichment analysis (GSEA) by…

A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

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A A A Algal Functional… Algal Functional Annotation Tool

Algal Functional Annotation Tool

A bioinformatics resource to functionally interpret gene lists and elucidate…

A bioinformatics resource to functionally interpret gene lists and elucidate underlying biological themes in silico using integrated annotation and expression data.

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A A A Gene Annotation… Gene Annotation Relationship Network Tools

GARNET Gene Annotation Relationship Network Tools

An integrative platform for diverse types of gene set analysis with annotation…

An integrative platform for diverse types of gene set analysis with annotation network navigation.

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A A A GeneTerm Linker GeneTerm Linker

GeneTerm Linker

Filters and links enriched output data identifying sets of associated genes and…

Filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance.

Web app
A A A ToppCluster ToppCluster

ToppCluster

A web server application that leverages a powerful enrichment analysis and…

A web server application that leverages a powerful enrichment analysis and underlying data environment for comparative analyses of multiple gene lists. ToppCluster generates heatmaps or connectivity…

Web app
A A A WEB-based GEne SeT… WEB-based GEne SeT AnaLysis Toolkit

WebGestalt WEB-based GEne SeT AnaLysis Toolkit

It is designed for functional genomic, proteomic and large-scale genetic…

It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are…

Web app
A A A Database for… Database for Annotation, Visualization and…

DAVID Database for Annotation, Visualization and Integrated Discovery

A web-based online bioinformatics resource that aims to provide tools for the…

A web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. DAVID has been used by researchers from more than 5000…

Desktop app
A A A Piano Piano

Piano

It is used for running gene set analysis with various statistical methods, from…

It is used for running gene set analysis with various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the piano package contains…

Web app
A A A FIDEA FIDEA

FIDEA

A server for the functional interpretation of differential expression analysis.…

A server for the functional interpretation of differential expression analysis. It is free and open to all users, and there is no login requirement.

Desktop app
A A A Ontologizer Ontologizer

Ontologizer

A Java application that can be used to perform statistical analysis for…

A Java application that can be used to perform statistical analysis for overrepresentation of Gene Ontology (GO) terms in sets of genes or proteins derived from an experiment. The Ontologizer…

Web app
A A A KEGG Orthology Based… KEGG Orthology Based Annotation System

KOBAS KEGG Orthology Based Annotation System

Its purpose is to identify statistically enriched pathways, diseases, and GO…

Its purpose is to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases.

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A A A Gene-set activity… Gene-set activity toolbox

GAT Gene-set activity toolbox

A comprehensive gene expression analysis tool that is implemented with data…

A comprehensive gene expression analysis tool that is implemented with data retriever, traditional data pre-processing, several gene-set analysis methods, network visualization and data mining tools.…

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A A A Gene Set Context… Gene Set Context Analysis

GSCA Gene Set Context Analysis

An open source software package to help researchers use massive amounts of…

An open source software package to help researchers use massive amounts of publicly available gene expression data (PED) to make discoveries. Users can interactively visualize and explore gene and…

Web app
A A A StemChecker StemChecker

StemChecker

A stemness analysis tool, based on the curation of nearly fifty published…

A stemness analysis tool, based on the curation of nearly fifty published stemness signatures defined by gene expression, RNAi screens, transcription factor (TF) binding sites, literature reviews and…

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A A A Interspecies… Interspecies Analysing Application using…

ISAAC Interspecies Analysing Application using Containers

Enables non-computer trained researchers to explore gene lists under different…

Enables non-computer trained researchers to explore gene lists under different biological aspects. From a user’s point of view, the main difference to other related projects is that the gene lists…

Web app
A A A Lists2Networks Lists2Networks

Lists2Networks

A user friendly web-based software system expected to significantly ease the…

A user friendly web-based software system expected to significantly ease the computational analysis process for experimental systems biologists employing high-throughput experiments at multiple…

Web app
A A A COFECO Deprecated COFECO

COFECO

A web-based tool for a composite annotation of protein complexes, KEGG pathways…

A web-based tool for a composite annotation of protein complexes, KEGG pathways and Gene Ontology (GO) terms within a class of genes and their orthologs under study. Widely used functional enrichment…

Web app
A A A DICS Deprecated DICS

DICS

A dynamic web repository of computationally predicted functional modules from…

A dynamic web repository of computationally predicted functional modules from the human protein-protein interaction network. It provides references to the CORUM, DrugBank, KEGG and Reactome pathway…

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