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Over-representation analysis (ORA) software tools | Gene expression

The immediate need for functional analysis of microarray gene expression data and the emergence of GO during that period gave rise to over-representation analysis (ORA), which statistically evaluates the fraction of genes in a particular pathway…
Blast2GO
Desktop

Blast2GO

A comprehensive bioinformatics tool for functional annotation of sequences and…

A comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes…

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g:Profiler
Web
Desktop

g:Profiler

Provides tool to perform functional enrichment analysis and mine additional…

Provides tool to perform functional enrichment analysis and mine additional information. g:Profiler is a web server that allows to characterize and manipulate gene lists of high-throughput genomics.…

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agriGO
Dataset

agriGO

Allows gene ontology (GO) analysis. agriGO is an analysis toolkit and database…

Allows gene ontology (GO) analysis. agriGO is an analysis toolkit and database for agricultural community. The database mainly contains analysis tools for processing with the agriGO v2.0-provided…

STEM
Desktop

STEM Short Time-series Expression Miner

A software program specifically designed for the analysis of short time series…

A software program specifically designed for the analysis of short time series microarray gene expression data. STEM implements unique methods to cluster, compare, and visualize such data. STEM also…

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Onto-Express
Web

Onto-Express

Mines the available functional annotation data and helps the researcher to find…

Mines the available functional annotation data and helps the researcher to find relevant biological processes. Onto-Express is able to translate lists of differentially regulated genes into…

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FatiGO
Web

FatiGO

Extracts Gene Ontology (GO) terms that are over- or under-represented in sets…

Extracts Gene Ontology (GO) terms that are over- or under-represented in sets of genes within the context of a genome-scale experiment. Allows to make functional profiling of genome-scale…

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EASE
Desktop

EASE Expression Analysis Systematic Explorer

Allows biological interpretation of gene lists that result from the analysis of…

Allows biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data. EASE automates the process of biological theme…

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WebGestalt
Web

WebGestalt WEB-based GEne SeT AnaLysis Toolkit

Permits the management, information retrieval, organization, visualization and…

Permits the management, information retrieval, organization, visualization and statistical analysis of large sets of genes. WebGestalt integrates functional enrichment analysis and information…

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GeneMerge
Web
Desktop

GeneMerge

Facilitates regulatory and metabolic pathway analysis, tests of population…

Facilitates regulatory and metabolic pathway analysis, tests of population genetic hypotheses and others. GeneMerge returns functional or categorical data associated with each gene in the study set…

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OE2GO
Desktop

OE2GO Onto-Express-to-go

Uses custom annotations to construct functional profiling. OE2GO enables the…

Uses custom annotations to construct functional profiling. OE2GO enables the researchers to use the functional annotations that are not yet in the public domain, by allowing them to be included in…

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FuncAssociate
Web

FuncAssociate

A web-based tool to help researchers use Gene Ontology attributes to…

A web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment.

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GOSSIP
Desktop

GOSSIP

Allows to find molecular functions, biological processes and cellular locations…

Allows to find molecular functions, biological processes and cellular locations significantly associated with gene groups. GOSSIP checks if processes, locations or whether functions described in gene…

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GOHyperGAll
Desktop

GOHyperGAll

Simplifies the usage of custom gene-to-gene-ontology (GO) mappings. GOHyperGAll…

Simplifies the usage of custom gene-to-gene-ontology (GO) mappings. GOHyperGAll is based on the GOstats package. This script computes for a given sample population of genes the enrichment test for…

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PageMan
Desktop

PageMan

Allows to investigate, annotate and condense high-throughput microarray data in…

Allows to investigate, annotate and condense high-throughput microarray data in the context of functional ontologies. PageMan is a graphical user interface (GUI) tool which permits to make different…

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GOexpress
Desktop

GOexpress

An R/Bioconductor package for identification and visualisation of gene…

An R/Bioconductor package for identification and visualisation of gene expression profiles that best classify sample groups according to any known experimental factor. In contrast to most GO term…

G T A T C G C T A
GOseq
Desktop

GOseq

An application for performing gene ontology (GO) analysis on RNA-seq data. GO…

An application for performing gene ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but…

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BayGO
Web

BayGO

Allows to search enriched terms from microarray data. BayGO permits to measure…

Allows to search enriched terms from microarray data. BayGO permits to measure the statistical association between differential gene expression and a given ontology term. It can present a statistical…

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GOFFA
Desktop

GOFFA Gene Ontology For Functional Analysis

Utilizes Gene Ontology (GO) for interpreting microarray data. GOFFA applies…

Utilizes Gene Ontology (GO) for interpreting microarray data. GOFFA applies statistical analysis in conjunction with intuitive visual display to present GO terms, trees and paths in a manner to…

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ProbCD
Web
Desktop

ProbCD Probabilistic Categorical Data analysis

Performs probabilistic categorical data analysis. ProbCD provides a level of…

Performs probabilistic categorical data analysis. ProbCD provides a level of modularity that makes it suitable to be incorporated by existing development efforts of integrative tools. It offers a…

goCluster
Desktop

goCluster

Enables scientists to employ annotation information, clustering algorithms and…

Enables scientists to employ annotation information, clustering algorithms and visualization tools in their array data analysis and interpretation strategy. goCluster is a solution that implements a…

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GOstats
Desktop

GOstats

Tests Gene Ontology (GO) terms for over or under-representation using either a…

Tests Gene Ontology (GO) terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate…

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ClueGO
Desktop

ClueGO

A Cytoscape plug-in that visualizes the non-redundant biological terms for…

A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers…

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GoMiner
Desktop

GoMiner

A tool for biological interpretation of 'omic' data – including…

A tool for biological interpretation of 'omic' data – including data from gene expression microarrays. GoMiner leverages the Gene Ontology (GO) to identify the biological processes,…

GOToolBox
Web

GOToolBox

Provides a series of programs allowing the functional investigation of groups…

Provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. GOToolBox allows 1) the identification of statistically relevant over- or…

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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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WEGO
Web

WEGO Web Gene Ontology Annotation Plot

A useful tool for plotting GO annotation results. It has been widely used in…

A useful tool for plotting GO annotation results. It has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project.

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GOEAST
Web

GOEAST Gene Ontology Enrichment Analysis Software Toolkit

A web based software toolkit providing easy to use, visualizable, comprehensive…

A web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from…

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GO::TermFinder
Desktop
Web

GO::TermFinder

A tool for finding significant GO terms shared among a list of genes from your…

A tool for finding significant GO terms shared among a list of genes from your organism of choice, helping you discover what they may have in common. GO::TermFinder can be used to draw conclusions…

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GOstat
Web

GOstat

Find statistically overrepresented GO terms within a group of genes. This…

Find statistically overrepresented GO terms within a group of genes. This program automatically obtains the GO annotations from a database and generates statistics of which annotations are…

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BiNGO
Desktop

BiNGO

A tool to determine which Gene Ontology (GO) categories are statistically…

A tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. BiNGO maps the predominant functional themes of a…

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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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mvGST
Desktop

mvGST

Supplies platform-independent tools helping to detect gene ontology (GO) terms…

Supplies platform-independent tools helping to detect gene ontology (GO) terms (gene sets) that are differentially active (up or down) in multiple contrasts of interest. mvGST utilizes meta-analytic…

GOAtools
Desktop

GOAtools Gene Ontology Association tools

Contains a library to process over- and under-representation of certain gene…

Contains a library to process over- and under-representation of certain gene ontology (GO) terms, based on Fisher's exact test. GOAtools is a python package that process the obo-formatted file…

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GoSurfer
Desktop

GoSurfer

An easy-to-use graphical exploration tool with built-in statistical features…

An easy-to-use graphical exploration tool with built-in statistical features that allow a rapid assessment of the biological functions represented in large gene sets. GoSurfer takes one or two…

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GenMAPP
Desktop

GenMAPP

A free computer application designed to visualize gene expression and other…

A free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. GenMAPP provides a means to rapidly…

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ChEA
Web

ChEA ChIP Enrichment Analysis

Provides an alternative way for researchers to analyze mRNA expression data in…

Provides an alternative way for researchers to analyze mRNA expression data in context of genome-wide transcription-factor ChIP-X experiments collected and organized into a prior knowledge database…

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GFINDer
Web

GFINDer Genome Function INtegrated Discoverer

Supplies large-scale lists of user-classified genes with the functional…

Supplies large-scale lists of user-classified genes with the functional profiles biologically characterizing the different gene classes in the list. GFINDer extracts annotations of different…

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JProGO
Web
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GOTM
Web

GOTM GOTree Machine

Provides a web-based and tree-based data mining environment for gene sets. GOTM…

Provides a web-based and tree-based data mining environment for gene sets. GOTM permits to interpret sets of interesting genes using Gene Ontology (GO) hierarchies. It can be useful in functional…

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EasyGO
Web

EasyGO

Performs Gene Ontology (GO)-based functional enrichment analysis. EasyGO is a…

Performs Gene Ontology (GO)-based functional enrichment analysis. EasyGO is a web-app that for crop and farm animal species, including Affymetrix GeneChips for 12 plants and 3 farm animals, together…

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OntologyTravers…
Web

OntologyTraverser

Allows Gene Ontology (GO) analysis of gene lists. OntologyTraverser considers…

Allows Gene Ontology (GO) analysis of gene lists. OntologyTraverser considers the paths from the root to each terminal annotation for genes in a list. It aims to locate gene-products (genes) to a…

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