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Created on: 12-Oct-2012   Last updated on: 12-Oct-2012  |  How to cite this?
Total resources - 153
A list of resources for functional analysis
Sravanthi Davuluri and Akhilesh Bajpai (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
ASSESS - Analysis of Sample Set Enrichment Scores
http://people.genome.duke.edu/assess
Functional annotation and statistical analysis across phenotypes: pathways, motifs and cytogenetics
1
ACT - Arabidopsis Co-Expression Tool
http://www.arabidopsis.leeds.ac.uk/ACT
Integrated functional analysis of Arabidopsis genes: batch ID conversion, GO, co-expression, expression patterns, cis-elements, etc.
9

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
Babelomics
http://www.babelomics.org  http://babelomics.bioinfo.cipf.es 
Functional annotation: GO, pathways, protein-interaction, miRNAs, copy number, transcription factors and binding sites, and microarray data-analysis
50
GENEMANIA
http://www.genemania.org
Functional association networks: GO terms, co-expression, domains, pathways, co-localization and genetic/protein-interactions
50
ATTED-II - Arabidopsis thaliana trans-factor and cis-element prediction database
http://atted.jp
Functional analysis of Arabidopsis genes: co-expression, co-localization, protein-interactions, pathways and transcription factors
70
Blast2GO
http://www.blast2go.com
Functional annotation of sequences (novel and annotated): GO, pathways, and various visualizations
82
CGI
http://www-rcf.usc.edu/~fsun/Programs/CGI/CGIMain.html
Gene prioritization based on gene expression and protein-interactions
87
CLEAN - CLustering Enrichment ANalysis
http://eh3.uc.edu/clean
Clustering and calculation of gene specific functional coherence scores to microarray data
87
BioLayout Express3D
http://www.biolayout.org
Gene networks based on relationships: disease, protein-interactions, pathways, gene expression, sequence similarity, regulatory cascades, etc.
96
AgBase
http://www.agbase.msstate.edu
Integrated tools for functional analysis of agricultural plant and animal gene products
98
Algal Functional Annotation Tool
http://pathways.mcdb.ucla.edu/algal
Integrated functional analysis of Algal genes: batch ID conversion, protein families, GO, pathways, domains, gene expression, etc.
98
ArrayXPath
http://www.snubi.org/software/ArrayXPath
Functional analysis of gene expression data: GO, pathways, disease, etc.
98
BCBC - Beta Cell Biology Consortium
http://www.betacell.org
Set of visualization and analysis tools focused on beta cells: gene network, meta-analysis, expression profile comparison, etc.
98
BioProfiling.de
http://www.bioprofiling.de
Integrated analysis of gene lists: GO, protein interactions, miRNAs, pathways, GWAS, metabolomics, etc.
98
ADGO
http://www.btool.org/ADGO2
Microarray data annotation: GO, pathways, transcription factor binding sites, miRNA, etc.
100

URL not working as on 18 Jan 2014 (confirmed on 3 Nov 2016)
Ali Baba - PubMed as a Graph
http://alibaba.informatik.hu-berlin.de
Search and visualize gene/protein functional associations: gene expression, tissue specificity, disease, pathways, protein-interactions, etc.
100
AMEN - Annotation, Mapping, Expression and Network
http://amen.sourceforge.net
Functional annotation: protein-interaction, chromosomal location and expression
100
ArrayProspector
http://www.bork.embl.de/ArrayProspector
Functional analysis of gene expression data: co-expression, protein-interactions and pathways
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
ArrayWiki
http://arraywiki.bme.gatech.edu
A platform for sharing microarray data repositories and meta-analysis
100
atBioNet
http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm
Gene network analysis: protein-interactions and pathways
100
BIANA - Biologic Interactions and Network Analysis
http://sbi.imim.es/web/BIANA.php
Functional annotation: functions, pathways, protein-interactions, etc.
100
BioLattice
http://cello.snubi.org/cgi-bin/biolattice/biolattice.cgi
Biological interpretation of gene expression data based on concept lattice analysis including GO and pathways
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
BiologicalNetworks/IntegromeDB/PathSys
http://biologicalnetworks.net
Integrated functional analysis: gene/protein-interactions, pathways, transcriptional regulation, GO, promoter analysis, diseases, structures, etc.
100
BioNetBuilder
http://err.bio.nyu.edu/cytoscape/bionetbuilder
A Cytoscape plugin for creation of biological networks: GO, protein-interactions, pathways, domains, etc.
100
BIOZON
http://www.biozon.org
Unified biological resource for integrated analysis: GO, pathways, protein-interactions, domains, gene expression, etc.
100
BITOLA - Biomedical Discovery Support System
http://ibmi.mf.uni-lj.si/bitola
Literature based biological associations: disease, tissue, pathology, pathway, drug, etc.
100
CancerResource
http://bioinf-data.charite.de/cancerresource
Functional annotation focused on cancer: GO, pathways, gene expression, drugs, protein-interactions, structures, etc.
100
CANDID - A candidate gene identification program
https://dsgweb.wustl.edu/hutz/index.html
Gene prioritization based on multiple factors: genetic linkage, sequence conservation, literature association, gene expression, user data, etc.
100
CARMAweb
https://carmaweb.genome.tugraz.at/carma
Microarray data annotation: pre-processing, differential expression, clustering and GO
100
Chilibot - Mining PubMed for relationships
http://www.chilibot.net
Find relationships between proteins/genes/keywords by searching PubMed
100
ClueGO
http://www.ici.upmc.fr/cluego
A Cytoscape plugin to visualize biological terms for a given set of genes in a functional network
100
cmap - Connectivity Map
http://www.broadinstitute.org/cmap
Find connections between biological entities: expression profiles, drug and gene interactions, diseases, etc.
100
COFECO - Composite Function Annotation Enriched by Protein Complex Data
http://piech.kaist.ac.kr/cofeco
Functional annotation: protein-complex, protein-interaction, GO, pathways, including term filtering and output comparisons
100

ConceptGen
http://conceptgen.ncibi.org/
Enrichment testing and concept mapping tool
100
ConsensusPathDB
http://cpdb.molgen.mpg.de
A web-resource focused on gene/protein-interactions and pathways including tools for network mapping, gene set and metabolite set analysis
100
CoPub
http://services.nbic.nl/copub/portal  http://services.nbic.nl/copub5 
Literature mining for co-occurring biomedical concepts: GO, disease, tissue, pathology, pathway, drug, etc.
100

URL not working as on 3 Nov 2016
CORNET - CORrelation NETworks
https://bioinformatics.psb.ugent.be/cornet
Functional annotation of Arabidopsis genes: co-expression, transcription regulation, protein-interactions, GO, pathways, etc.
100
DAVID - Database for Annotation, Visualization and Integrated Discovery
http://david.abcc.ncifcrf.gov
Comprehensive functional annotation: GO, pathways, protein-interactions, SNPs, gene expression, diseases, domains, etc. including over-representation and statistical enrichment
100
DEEP - Differential Expression Effector Prediction
http://deep.bioinf.med.uni-goettingen.de
Differential expression with signaling networks
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
DIR
http://cbc.case.edu/dir
Functional relationships of disease genes vs. candidate genes: protein-interaction, gene expression, pathway, etc.
100
DiscoverySpace
http://www.bcgsc.ca/platform/bioinfo/software/ds
A platform for high-throughput data analysis
100
DPBE - Dragon Plant Biology Explorer
http://research.i2r.a-star.edu.sg/DRAGON/ME2
Functional associations of Arabidopsis genes: literature keywords, GO, pathways, enzymes, gene/protein-interactions, etc.
100
DRAGON - Database Referencing of Array Genes ONline
http://pevsnerlab.kennedykrieger.org/dragon.htm
Integrated functional analysis: gene expression, localization, domains, function, pathways, etc.
100
DTFAM - Dragon TF Association Miner
http://research.i2r.a-star.edu.sg/DRAGON/TFAM
Functional associations: literature keywords, GO, diseases, transcription factors, etc.
100
eGIFT - Extracting Gene Information From Text
http://biotm.cis.udel.edu/eGIFT
Find relationships (informative terms: iTerms) for gene(s) from literature
100
Endeavour
http://www.esat.kuleuven.be/endeavour
Gene prioritization based on multiple factors: protein-interactions, gene expression, transcriptional regulation, localization, pathways, GO, literature, etc.
100
Enrichment Map
http://baderlab.org/Software/EnrichmentMap
Plugin for functional enrichment and visualizations: GSEA, GO, pathways, etc.
100
ERGO Genome Analysis & Discovery System
https://ergo.integratedgenomics.com
Systems biology platform for analysis of organisms with many integrated tools
100
ermineJ
http://www.chibi.ubc.ca/ermineJ
Gene set analysis tool: ranking, over-representation, GO, etc.
100
EXPANDER - EXpression Analyzer and DisplayER
http://acgt.cs.tau.ac.il/expander
Microarray data annotation: pre-processing, differential expression, clustering, GO, pathways, transcription factor binding sites, miRNA, etc.
100
Expression Profiler
http://www.bioinf.ebc.ee/EP  http://ep.ebi.ac.uk 
Set of gene expression analysis tools: clustering, GO, protein-interactions, sequence patterns, etc.
100

URL not working as on 20 Jan 2014; getting error 403 (confirmed on 3 Nov 2016)
FIVA - Functional Information Viewer and Analyzer
http://bioinformatics.biol.rug.nl/standalone/fiva
Functional profile construction based on similar gene expression pattern: pathways, GO, domain, generic functions, etc.
100
FunCoup - Networks of functional coupling
http://FunCoup.sbc.su.se
Functional relationships: gene expression, interaction, localization, etc.
100
FunNet - Transcriptional Networks Analysis
http://www.funnet.info
Transcriptional interactions and co-expression analysis of gene expression data
100
FunSpec - Functional Specification
http://funspec.med.utoronto.ca
Functional annotation of yeast genes: GO, domains, pathways, localization, protein-interactions, etc.
100
g:Profiler
http://biit.cs.ut.ee/gprofiler
Functional profiling: interactions, gene expression, GO, pathways, diseases, etc.
100
G2D - Genes2Diseases
http://g2d2.ogic.ca/
Functional analysis focused on genes' inherited disease relationships including GO, protein-interactions and literature
100
Gaggle
http://gaggle.systemsbiology.net
Integrated tools for functional analysis: gene expression, protein-interactions, pathways, etc.
100
GARBAN - Genomic Analysis and Rapid Biological Annotation
http://garban.tecnun.es
Functional classification of genes: differential expression, GO, pathways, etc.
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
GATHER - Gene Annotation Tool to Help Explain Relationships
http://gather.genome.duke.edu
Functional annotation of gene sets: GO, MeSH, pathways, protein-binding, miRNA, transcription factors/binding sites, etc.
100
Gazer - Gene Set Analyzer
http://integromics.kobic.re.kr/Gazer
Microarray data annotation: GO, pathways, domain, etc.
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
GEMS - Gene Expression Metasignatures
http://www.nursa.org/gems
A search engine to query the meta-analysis results
100
GEM-TREND - Gene Expression data Mining Toward RElevant Network Discovery
http://cgs.pharm.kyoto-u.ac.jp/services/network/index.php
A tool for gene expression data retrieval and network visualizations
100
GenAge - The Ageing Gene Database
http://genomics.senescence.info/genes
A resource of manually curated genes related to ageing, including tools for functional analysis: GO, protein-interactions, localization, gene expression, literature, etc.
100
Genapha - genomic applications for humanity
http://genapha.icapture.ubc.ca
Functional analysis tool for allergy and asthma research: pathways, SNPs and GO
100
GenCLiP - Gene Cluster with Literature Profiles
http://www.bioinformatics.org/genclip  http://genclip.sourceforge.net http://www.genclip.com
A literature mining tool to identify pathogenesis profiles and specific pathways, including co-occurrence networks
100
Gendoo - Gene, Disease Features Ontology-based Overview System
http://gendoo.dbcls.jp
Functional relationships: diseases, drugs, biological phenomena
100
Gene3D - Structure Assigned to Genomes
http://gene3d.biochem.ucl.ac.uk
A resource to explore protein domains, families, structures and protein-interactions
100
GeneAnswers - Integrated Interpretation of Genes
http://www.bioconductor.org/packages/2.6/bioc/html/GeneAnswers.html
Integrated statistical analysis for specified categories: protein-interactions, GO, pathways, transcriptional regulation, etc.
100
GeneBrowser
http://orbit.nlm.nih.gov/resource/genebrowser
Identify common biological characteristics: GO, pathways, protein-interactions, gene expression, genomic elements, literature, etc.
100
GeneCoDis - Gene annotations Co-occurrence Discovery
http://genecodis.cnb.csic.es
Enrichment and comparative analysis of genes based on co-occurrences of annotations: GO, pathways, literature, diseases, miRNA, transcription factors, etc.
100
GeneDistiller
http://www.genedistiller.org
Gene prioritization based on multiple factors: GO, pathways, diseases, expression, interactions, domains, localization, etc.
100
GeneNet - Modeling and Inferring Gene Networks
http://strimmerlab.org/software/genenet/
An R package for gene association networks: diseases, GO, protein-isoforms, etc.., and user keywords
100
GenePattern
http://www.broadinstitute.org/cancer/software/genepattern
Integrated analysis tools: differential expression, class prediction, pathways, etc.
100
GenePro
http://wodaklab.org/genepro
Plugin for deriving functional modules: GO, localization, evolutionary conservation, gene/protein-interactions, mRNA expression, etc.
100
GeneRank
http://bodymap.ims.u-tokyo.ac.jp/
Gene prioritization based on gene expression and GO annotations
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
GeneRanker
http://cbioc.eas.asu.edu/generanker  http://www.generanker.org 
Identify and annotate gene-disease relationships by mining the biomedical literature
100
Genes2Fans
http://actin.pharm.mssm.edu/genes2FANs
Functional association networks: protein-interactions, pathways, miRNAs, phenotypes, domains, metabolites, etc.
100
GeneTrail
http://genetrail.bioinf.uni-sb.de
Gene set analysis: GSEA, pathways, over-representation, GO, etc.
100
GeneXplain
http://www.genexplain.com
Unified access to a broad range of bioinformatics tools
100
GenMAPP - Gene Map Annotator and Pathway Profiler
http://www.genmapp.org
Functional annotation of gene expression and other data: GO and pathways, and overlay expression data
100
Genome Network Platform
http://genomenetwork.nig.ac.jp/index_e.html
Genome, transcription factors/binding sites, and protein-interactions
100
Genomics Portals - Laboratory for Statistical Genomics and Systems Biology
http://GenomicsPortals.org
Genomic data mining, integrating functional knowledgebase and analysis tools: GO, gene expression, protein-interactions, pathways, transcription regulation, literature, etc.
100
GenSensor Suite
http://bio.ccs.miami.edu/cgi-bin/GSS/Documentation.cgi
Functional associations: over-representation, GO, protein-interactions, PubMed
100
GenTrepid
http://www.gentrepid.org
Gene prioritization based on pathways and disease relationships, including protein-interactions, domains and structures
100
GEPAT - Genome Expression Pathway Analysis Tool
http://gepat.sourceforge.net
Integrated analysis of transcriptome data: domains, protein interactions, literature references, pathways and microrarray data-analysis
100
GESBAP - GEne Set Based Analysis of Polymorphisms
http://bioinfo.cipf.es/gesbap
Gene or SNP data functional analysis: GO, pathways, genetic/protein-interactions
100
GFINDer - Genome Function INtegrated Discoverer
http://www.medinfopoli.polimi.it/GFINDer
Functional annotation: GO, pathways, protein-interaction, genetic disorders, domains, etc., including statistical analysis
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
GOAPhAR - Gene Ontology, Annotations and Pathways for Array Research
http://bioinformatics.kumc.edu/goaphar
Functional annotation: gene/protein annotations, protein-interactions, pathways and GO
100
GoCat - Gene Ontology Categorizer
http://eagl.unige.ch/GOCat/
A tool for categorization of multiple genes based on GO and SwissProt keywords
100
godisease
http://www.godisease.com
Gene associations: diseases, GO, protein-isoforms, etc.., and user keywords
100
GOFFA
http://edkb.fda.gov/webstart/arraytrack/
GO based functional analysis of genomic and proteomic data
100
GPSy
http://gpsy.genouest.org
Gene function prediction of conserved developmental processes by a cross-species prioritization system
100
GRAMENE
http://www.gramene.org
An information resource and multiple analysis system for grass genomics
100
GRANITE - Gene RelAtional Network of InTeracting Elements
http://bioinformatics.wustl.edu/webTools/GraniteGeneSearch.do
Gene relational networks: gene/protein-interactions, pathways, transcription factor targets, GO, gene expression, literature, etc.
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
Graphle
http://sonorus.princeton.edu/graphle
Biological network creation based on functional annotation: GO, protein-interactions, etc.
100
GraphWeb
http://biit.cs.ut.ee/graphweb
Graph-based analysis of biological networks: GO, protein-interactions, pathways, motifs, orthology, etc.
100
GSA - Gene Set Analysis
http://www-stat.stanford.edu/~tibs/GSA
An R package for the functional analysis based on gene expression and pathways
100
GSEA - Gene Set Enrichment Analysis
http://www.broadinstitute.org/gsea
A platform to define genes statistically significant between two groups
100
G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools
http://bioinformatics.clemson.edu/G-SESAME
Functional similarity between genes or GO terms
100
GVIZ - Co-expression networks visualization tool
http://urbm-cluster.urbm.fundp.ac.be/webapps/gviz
Network visualization and exploration: co-expression, protein-interactions, GO, domains, literature, pathways, etc.
100
Hanalyzer - high-throughput analyzer
http://hanalyzer.sourceforge.net
Integrated functional analysis: GO, pathways, protein-interactions, domains, literature co-occurrence, etc.
100
HEAT - H-InvDB Enrichment Analysis Tool
http://h-invitational.jp/HEAT
Enriched features for a given set of genes including GO, domains, motifs, protein-interactions
100

KOBAS - KEGG Orthology Based Annotation System
http://kobas.cbi.pku.edu.cn/home.do
Annotation and identification of statistically enriched pathways and diseases
100
L2L
http://depts.washington.edu/l2l
Find biological significance in microarray data by comparing with existing data: co-expression, GO, disease, miRNA, protein-interactions, etc.
100
l2n - Lists2Networks
http://www.lists2networks.org
Integrated functional analysis: co-expression, co-annotation, protein-interactions, GO, pathways, domains, miRNA, metabolites, etc.
100

URL not working as on 20 Jan 2014
LIBGS - A MATLAB Package for Gene Selection
http://users.cis.fiu.edu/~yzhan004/genesel.html
A Matlab package for gene selection based on several selection algorithms
100
MAGIA - MiRNA And Genes Integrated Analysis web tool
http://gencomp.bio.unipd.it/magia2
Integrated analysis of gene expression and miRNA data: functional enrichment, miRNA targets, transcription factors, etc.
100
MassNet
http://massnet.kr
Functional annotation of mass-spec data: protein-interactions, physico-chemical analysis, pathways, GO, etc.
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
MAVEN - Management, Analysis, Visualization and rEsults shariNg
http://cbc.case.edu/maven
Functional analysis of genome-wide association (GWA) data: data filtering, functional roles of SNPs, pathways, etc.
100
MEDIE
http://www.nactem.ac.uk/tsujii/medie
Biomedical correlations from literature
100
MEM - Multi Experiment Matrix
http://biit.cs.ut.ee/mem
Integrated analysis of genes: gene expression comparisons with existing microarray data, GO, disease, miRNA, protein-interactions, etc.
100
MetaGP - MetaGeneProfiler
http://metagp.ism.ac.jp
Differential expression and significance analysis from microarray data: GO, pathways and transcription modules
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
MetaRanker
http://www.cbs.dtu.dk/services/metaranker
Functional analysis of genome-wide association (GWA) data: linkage studies, protein-interactions, disease-similarity, gene expression, etc.
100
MILANO - Microarray Literature-based Annotation
http://bioinformatics.ekmd.huji.ac.il/milano
Gene set analysis: automated search in PubMed to find out co-occurrences of search terms
100
NetAtlas
http://netatlas.sourceforge.net
A Cytoscape plugin for network analysis using gene expression data: tissue-defined networks, correlated expression, cell-signaling, etc.
100
Netview
http://netview.tigem.it
A tool to explore gene regulatory networks, including GO prediction and gene signature analysis
100
NW - NetWalker
https://netwalkersuite.org
A network analysis tool: data normalization, clustering, protein-interactions, GO, etc.
100
PaLS - Pathway and Literature Strainer
http://pals.bioinfo.cnio.es
Find common biological annotations: PubMed references, GO and pathways
100
PANTHER - Protein ANalysis THrough Evolutionary Relationships
http://www.pantherdb.org
A resource for classification of genes by functions, and additional annotation and analysis of data: orthology, GO, pathways, gene expression, evolution, etc.
100
PathCluster
http://www.systemsbiology.co.kr/PathCluster
Gene set clustering based on functional annotation: GO, motifs, transcription regulation, molecular-interactions
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
PathEx
http://urbm-cluster.urbm.fundp.ac.be/webapps/pathex/geo/pathex.php
Custom selection of gene expression data and functional analysis: protein-interactions, literature, pathways, functions, etc.
100
PathMAPA -
http://bioinformatics.med.yale.edu/pathmapa.htm
Search and manipulate Arabidopsis microarray data: gene expression, enzymes, pathways eith expression overlay, statistical analysis, etc.
100

Website states that the resource is no longer supported, as on 18 Jan 2014. The given URL directs to a different webpage, as on 3 Nov 2016
Pathvar - Microarray analysis of pathway expression variance
http://pathvar.embl.de
Functional annotation: GO, pathways, protein-interaction and domains
100
PathwayLinker
http://pathwaylinker.org
Interactions and associated signaling pathways for a given set of genes, with links to other resources
100
PINTA - Gene Prioritization by Network Analysis
http://www.esat.kuleuven.be/pinta
Gene prioritization based on differential expression and gene/protein-interaction networks
100
Plant MetGenMAP
http://bioinfo.bti.cornell.edu/cgi-bin/MetGenMAP/home.cgi
Analysis and visualizations from gene expression and/or metabolite profiles: pathways changed and enriched GO
100
PolyMAPr - Polymorphism Mining and Annotation Programs
http://pharmacogenomics.wustl.edu
Functional annotation of polymorphism data: functional effects of coding region SNPs, putative transcription factor binding sites, splicing sites, etc.
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
PosMed
http://omicspace.riken.jp/PosMed
Genes prioritization with an artificial neural network, and gene ranking based on biomolecular interactions and disease associations
100
Prioritizer - positional candidate gene prioritization
http://www.prioritizer.nl
Functional analysis of genome-wide association (GWA) data: co-expression from microarray, protein-interactions, GO, pathways, etc.
100

URL directs to a different webpage (as on 3 Nov 2016)
ProbFAST - Probabilistic Functional Analysis System Tool
http://gdm.fmrp.usp.br/probfast
Gene expression analysis with functional annotation including GO and pathways
100
ProcessDB
http://www.integrativebioinformatics.com/processdb.html
A tool for modeling biological systems
100
ProDiGe - Prioritization of disease genes
http://cbio.ensmp.fr/~jvert/svn/prodige/html
Disease gene prioritization and functional annotation: disease associations, gene expression, protein-interactions, domains, transcriptional motifs and literature
100
RACE - Remote Analysis Computation for gene Expression data
http://race.unil.ch
Microarray data annotation: pre-processing, differential expression and GO
100
SAFE - Significance Analysis of Function and Expression
http://bioconductor.org/packages/2.0/bioc/html/safe.html
An R package for the functional analysis: GO, pathways and gene expression
100
Microarray data annotation: differential expression, GO, pathways, genetic interactions, etc.
100
SIGNATURE - A Workbench for Gene Expression Signature Analysis
http://genepattern.genome.duke.edu/signature  http://www.bioinformatics.org/signature 
A tool to find and predict signature sets from gene expression data based on activation of pathways, create subtypes and user specific sets
100
Protein interaction resource with multiple annotations and functional analyses: pathways, GO, domains, and interaction-activity and clustering
100
Candidate gene prioritization based on ranking of multiple factors: phenotypes, neighbor genes, GO, domains, gene expression, sequences and chromosomal location
100
TAFFEL - Independent Enrichment Analysis of gene sets
http://www.oppi.uef.fi/bioinformatics/taffel
Clustering gene sets to sub-groups based on GO and transcription regulators
100
TargetMine - Data warehouse for target discovery
http://targetmine.nibio.go.jp
Functional enrichment analysis: disease ontology, GO, pathways, protein-interactions, drug-targets, transcription factors, enzymes, etc.
100
Taverna
http://www.taverna.org.uk
A suite to create, edit, and execute workflows with multiple analysis: pathways, sequences, etc.
100
TOM - Transcriptome of OMIM
http://www-micrel.deis.unibo.it/~tom
A tool for extraction of candidate genes for hereditary diseases and functional analysis: disease-relationships, GO, co-expression, etc.
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
ToppCluster
http://toppcluster.cchmc.org
Feature enrichment analysis for multiple genes
100
ToppGene Suite
http://toppgene.cchmc.org/
Gene set enrichment analysis: miRNAs, GO, protein-interactions, pathways, pharmacome, literature co-citations, transcription factors/binding sites, etc.
100
T-Profiler
http://hjbweb.bio.columbia.edu/t-profiler/index.html
Microarray data annotation: consensus motifs, transcription modules, aneuploidy and GO
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
TS-CoExp
http://109.233.127.52/ts-coexp/index
Functional annotation and disease gene prioritization: conserved co-expression networks, functions, genetic disease relationships, etc.
100
VAVIEN - Prioritize disease genes
http://www.diseasegenes.org
Candidate disease genes prioritization based on topological similarity of proteins in interaction networks
100

URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016)
VisANT - Integrative Visual Analysis Tool for Biological Networks and Pathways
http://visant.bu.edu
Integrated visual data-mining and network analysis: GO, protein-interactions, pathways with expression overlay, etc.
100
VISTA
http://genome.lbl.gov/vista/index.shtml
A suite for comparative analysis of genomic sequences
100
WebGestalt - WEB-based GEne SeT AnaLysis Toolkit
http://bioinfo.vanderbilt.edu/webgestalt
Gene set analysis: GO, pathways, gene expression, etc.
100
WebGimm - Cluster Analysis Server
http://www.eh3.uc.edu/gimm/webgimm
Clustering and functional enrichment of microarray data including pre-processing
100
WhichGenes
http://www.whichgenes.org
Gene set creation and comparison based on biological annotations
100
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