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…
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g:Profiler
Web

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…

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Enrichr
Web
Mobile

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…

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GeneWeaver
Web

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…

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DAVID
Web

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…

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Ontologizer
Desktop

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…

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GeneTrail
Web

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,…

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IMP
Web

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…

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piano
Desktop

piano Platform for Integrated Analysis of Omics data

Performs gene set analysis (GSA) using various statistical methods, from…

Performs gene set analysis (GSA) using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The piano package contains functions for combining…

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RCAS
Web
Desktop

RCAS RNA Centric Annotation System

Provides dynamic genome annotations for custom input files that contain…

Provides dynamic genome annotations for custom input files that contain transcriptomic regions. RCAS enables flexible usage and convenient integration with other bioinformatics workflows. It is not…

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KOBAS
Web

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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GSEA
Desktop

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…

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GeneCodis
Web

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…

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GeneSCF
Desktop

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…

Babelomics
Desktop
Web

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…

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JEPETTO
Desktop

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…

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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,…

GenCLiP
Web

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…

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ToppCluster
Web

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…

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PlantGSEA
Web

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…

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Lynx
Web

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…

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EDDY
Desktop

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…

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ABAEnrichment
Desktop

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…

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GSA-Lightning
Desktop

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…

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GiANT
Desktop

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…

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R spider
Web

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…

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SetRank
Desktop

SetRank

Permits to eliminate many false positive hits in gene set enrichment analysis…

Permits to eliminate many false positive hits in gene set enrichment analysis (GSEA). SetRank discards gene sets that have initially been flagged as significant, if their significance is only due to…

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GSAR
Desktop

GSAR Gene Set Analysis in R

Implements self-contained multivariate non-parametric statistical methods…

Implements self-contained multivariate non-parametric statistical methods testing a complex null hypothesis against specific alternatives, such as differences in mean (shift), variance (scale), or…

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FIDEA
Web

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.

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CAsubtype
Desktop

CAsubtype

Identifies gene sets for cancer subtype identification and clinical outcome…

Identifies gene sets for cancer subtype identification and clinical outcome prediction. CAsubtype integrates more than 13,000 annotated gene sets and provides a comprehensive repertoire of candidates…

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MORPHIN
Web

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.…

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PathwAX
Web

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…

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GSCA
Desktop
Web

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…

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NetVenn
Web

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…

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GeneAnalytics
Web

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…

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FUNNEL-GSEA
Desktop
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ASSIGN
Desktop

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.…

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stringgaussnet
Desktop

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…

dslice
Desktop

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…

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NEAT
Desktop

NEAT Network Enrichment Analysis Test

Aims to overcome some limitations of existing resampling-based tests. The main…

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 number of links between two gene sets A and B…

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rapidGSEA
Desktop

rapidGSEA rapid Gene Set Enrichment Analysis

Facilitates permutation-based gene set enrichment analysis and for commonly…

Facilitates 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 tool using…

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Gitools
Web

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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Genes2Networks
Web

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…

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QuSAGE
Desktop

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…

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StemChecker
Web

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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TargetMine
Dataset

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…

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RNAModR
Desktop

RNAModR

Analyses and visualises the transcriptome-wide distribution of mRNA…

Analyses and visualises the transcriptome-wide distribution of mRNA modifications. RNAModR provides functions to map lists of genomic loci of RNA modifications to a reference mRNA transcriptome, and…

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MULSEA
Desktop

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…

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XGSA
Desktop

XGSA

Takes the cross-species homology mapping into consideration when doing gene set…

Takes the cross-species homology mapping into consideration when doing gene set analysis. Simulation experiments confirm that XGSA can avoid false positive discoveries, while maintaining good…

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WormExp
Web

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…

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npGSEA
Desktop

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…

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ArrayPlex
Desktop

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…

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YunBe
Cloud

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.

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ADGO
Web

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…

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Algal…
Web

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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Lists2Networks
Web

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…

SANTA
Desktop

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…

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FungiFun
Web

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…

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GeneTerm Linker
Web

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.

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ChIP-Enrich
Desktop
Web

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…

xCell
Web

xCell

Performs cell type enrichment analysis from gene expression data for 64 immune…

Performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. xCell is a gene signatures-based method learned from thousands of pure cell types from various…

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WTFgenes
Desktop
Web

WTFgenes What’s The Function of these genes?

Interprets experimentally-identified lists of genes. WTFgenes uses…

Interprets experimentally-identified lists of genes. WTFgenes uses hypergeometric and model-based approaches. It permits to know what is the function of different genes thanks to Bayesian Term…

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TopKLists
Desktop

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…

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Constellation…
Web

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…

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GeneSetDB
Web

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.

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mgsa
Desktop

mgsa Model-based gene set analysis

Reduces the number of redundant categories returned by the gene category…

Reduces the number of redundant categories returned by the gene category analysis. mgsa employs probabilistic inference via a Metropolis-Hasting algorithm to estimate the probability of categories to…

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GlobalANCOVA
Desktop

GlobalANCOVA

Summarizes the individual gene-wise linear models to a group statement.…

Summarizes the individual gene-wise linear models to a group statement. GlobalANCOVA is an ANOVA-based sum of squares that offers data and functions as well as a vignette to guide the user through…

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PAGER
Dataset

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…

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RDAVIDWebServic…
Desktop

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…

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GEO2Enrichr
Web

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.…

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RAMONA
Web

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.

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RIDDLE
Web

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…

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GEPAT
Web

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…

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AtCAST
Web

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…

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WebGestalt
Web

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…

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BubbleGUM
Desktop

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…

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ErmineJ
Desktop

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…

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WhichGenes
Web

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…

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ProfCom
Web

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…

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RuleGO
Web

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…

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KEGG Mapper
Web

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…

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Enrichment Map
Desktop

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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FGSEA
Desktop

FGSEA Fast Gene Set Enrichment Analysis

Implements a special algorithm to calculate the empirical enrichment score null…

Implements a special algorithm to calculate the empirical enrichment score null distributions simultaneously for all the gene set sizes. FGSEA is a fast gene set enrichment analysis (FGSEA) method…

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GeneAnswers
Desktop

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…

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Tribe
Web

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…

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GAT
Web

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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iPEAP
Desktop

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…

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NetPathMiner
Desktop

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.

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Q-Gen
Desktop

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…

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GSVA
Desktop

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…

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GARNET
Web

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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GenMiner
Desktop

GenMiner

Allows to analyze genomic data. GenMiner allows the analysis of datasets…

Allows to analyze genomic data. GenMiner allows the analysis of datasets integrating multiple sources of biological data represented as both discrete values, such as gene annotations, and continuous…

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Connections…
Web

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.

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PhenoFam
Web

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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REGNET
Web

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.

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MIGSA
Desktop

MIGSA Massive and Integrative Gene Set Analysis

Allows to perform a massive and integrative gene set analysis over several…

Allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. MIGSA provides a common gene expression analytic framework that grants a…

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cWords
Web
Desktop

cWords

Regulates motif discovery in differential case–control mRNA expression…

Regulates motif discovery in differential case–control mRNA expression datasets. cWords can identify potential siRNA off-target binding. It is based on rigorous statistical methods that demonstrate…

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GLAD
Dataset

GLAD Gene List Annotation for Drosophilia

Lists functionally related Drosophila genes, e.g. based on protein domains…

Lists functionally related Drosophila genes, e.g. based on protein domains (kinases, transcription factors, etc.) or cellular function (e.g. autophagy, signal transduction). GLAD relies on different…

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AtlasRDF
Desktop

AtlasRDF

Query the Gene Expression AtlasRDF data at the European Bioinformatics…

Query the Gene Expression AtlasRDF data at the European Bioinformatics Institute using genes, experimental factors (such as disease, cell type, compound treatments), pathways and proteins. AtlasRDF…

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clipper
Library

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…

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EGSEA
Desktop

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…

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GsNetCom
Web

GsNetCom Gene sets Network Communication

Provides a batch tool for user. GsNetCom is a web-based toolkit to measure the…

Provides a batch tool for user. GsNetCom is a web-based toolkit to measure the functional association between two gene sets. It is based on a method called corrected cumulative rank score(CCRS) which…

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PCP
Desktop

PCP Pattern Classification Program

Implements leading pattern classification and gene selection algorithms and…

Implements leading pattern classification and gene selection algorithms and incorporates cross-validation estimation of classifier performance. PCP is an open-source machine learning program for…

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DroPhEA
Web

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…

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MamPhEA
Web

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…

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EnrichNet
Web

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.

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ConceptGen
Web

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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LRpath
Web

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.…

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SAM-GS
Desktop

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.…

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Kiwi
Desktop
Web

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.…

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GO2MSIG
Desktop
Web

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.

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ISAAC
Web

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…

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gsGator
Web

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.

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POEAS
Web

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…

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PathExpand
Web

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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FunSpec
Web

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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GeneCruiser
Web

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…

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COFECO
Web

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…

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DICS
Web

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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