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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)

S.NoResources
Short description*Rank by usage frequency Click to Edit / Add comments
1ASSESS - Analysis of Sample Set Enrichment Scores
http://people.genome.duke.edu/assess
Functional annotation and statistical analysis across phenotypes: pathways, motifs and cytogenetics
1
2ACT - 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)
3Babelomics
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
4GENEMANIA
http://www.genemania.org
Functional association networks: GO terms, co-expression, domains, pathways, co-localization and genetic/protein-interactions
50
5ATTED-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
6Blast2GO
http://www.blast2go.com
Functional annotation of sequences (novel and annotated): GO, pathways, and various visualizations
82
7CGI
http://www-rcf.usc.edu/~fsun/Programs/CGI/CGIMain.html
Gene prioritization based on gene expression and protein-interactions
87
8CLEAN - CLustering Enrichment ANalysis
http://eh3.uc.edu/clean
Clustering and calculation of gene specific functional coherence scores to microarray data
87
9BioLayout Express3D
http://www.biolayout.org
Gene networks based on relationships: disease, protein-interactions, pathways, gene expression, sequence similarity, regulatory cascades, etc.
96
10AgBase
http://www.agbase.msstate.edu
Integrated tools for functional analysis of agricultural plant and animal gene products
98
11Algal 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
12ArrayXPath
http://www.snubi.org/software/ArrayXPath
Functional analysis of gene expression data: GO, pathways, disease, etc.
98
13BCBC - 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
14BioProfiling.de
http://www.bioprofiling.de
Integrated analysis of gene lists: GO, protein interactions, miRNAs, pathways, GWAS, metabolomics, etc.
98
15ADGO
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)
16Ali 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
17AMEN - Annotation, Mapping, Expression and Network
http://amen.sourceforge.net
Functional annotation: protein-interaction, chromosomal location and expression
100
18ArrayProspector
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)
19ArrayWiki
http://arraywiki.bme.gatech.edu
A platform for sharing microarray data repositories and meta-analysis
100
20atBioNet
http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm
Gene network analysis: protein-interactions and pathways
100
21BIANA - Biologic Interactions and Network Analysis
http://sbi.imim.es/web/BIANA.php
Functional annotation: functions, pathways, protein-interactions, etc.
100
22BioLattice
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)
23BiologicalNetworks/IntegromeDB/PathSys
http://biologicalnetworks.net
Integrated functional analysis: gene/protein-interactions, pathways, transcriptional regulation, GO, promoter analysis, diseases, structures, etc.
100
24BioNetBuilder
http://err.bio.nyu.edu/cytoscape/bionetbuilder
A Cytoscape plugin for creation of biological networks: GO, protein-interactions, pathways, domains, etc.
100
25BIOZON
http://www.biozon.org
Unified biological resource for integrated analysis: GO, pathways, protein-interactions, domains, gene expression, etc.
100
26BITOLA - Biomedical Discovery Support System
http://ibmi.mf.uni-lj.si/bitola
Literature based biological associations: disease, tissue, pathology, pathway, drug, etc.
100
27CancerResource
http://bioinf-data.charite.de/cancerresource
Functional annotation focused on cancer: GO, pathways, gene expression, drugs, protein-interactions, structures, etc.
100
28CANDID - 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
29CARMAweb
https://carmaweb.genome.tugraz.at/carma
Microarray data annotation: pre-processing, differential expression, clustering and GO
100
30Chilibot - Mining PubMed for relationships
http://www.chilibot.net
Find relationships between proteins/genes/keywords by searching PubMed
100
31ClueGO
http://www.ici.upmc.fr/cluego
A Cytoscape plugin to visualize biological terms for a given set of genes in a functional network
100
32cmap - Connectivity Map
http://www.broadinstitute.org/cmap
Find connections between biological entities: expression profiles, drug and gene interactions, diseases, etc.
100
33COFECO - 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
34ConceptGen
http://conceptgen.ncibi.org/
Enrichment testing and concept mapping tool
100
35ConsensusPathDB
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
36CoPub
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
37CORNET - CORrelation NETworks
https://bioinformatics.psb.ugent.be/cornet
Functional annotation of Arabidopsis genes: co-expression, transcription regulation, protein-interactions, GO, pathways, etc.
100
38DAVID - 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
39DEEP - 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)
40DIR
http://cbc.case.edu/dir
Functional relationships of disease genes vs. candidate genes: protein-interaction, gene expression, pathway, etc.
100
41DiscoverySpace
http://www.bcgsc.ca/platform/bioinfo/software/ds
A platform for high-throughput data analysis
100
42DPBE - 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
43DRAGON - Database Referencing of Array Genes ONline
http://pevsnerlab.kennedykrieger.org/dragon.htm
Integrated functional analysis: gene expression, localization, domains, function, pathways, etc.
100
44DTFAM - Dragon TF Association Miner
http://research.i2r.a-star.edu.sg/DRAGON/TFAM
Functional associations: literature keywords, GO, diseases, transcription factors, etc.
100
45eGIFT - Extracting Gene Information From Text
http://biotm.cis.udel.edu/eGIFT
Find relationships (informative terms: iTerms) for gene(s) from literature
100
46Endeavour
http://www.esat.kuleuven.be/endeavour
Gene prioritization based on multiple factors: protein-interactions, gene expression, transcriptional regulation, localization, pathways, GO, literature, etc.
100
47Enrichment Map
http://baderlab.org/Software/EnrichmentMap
Plugin for functional enrichment and visualizations: GSEA, GO, pathways, etc.
100
48ERGO Genome Analysis & Discovery System
https://ergo.integratedgenomics.com
Systems biology platform for analysis of organisms with many integrated tools
100
49ermineJ
http://www.chibi.ubc.ca/ermineJ
Gene set analysis tool: ranking, over-representation, GO, etc.
100
50EXPANDER - 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
51Expression 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)
52FIVA - 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
53FunCoup - Networks of functional coupling
http://FunCoup.sbc.su.se
Functional relationships: gene expression, interaction, localization, etc.
100
54FunNet - Transcriptional Networks Analysis
http://www.funnet.info
Transcriptional interactions and co-expression analysis of gene expression data
100
55FunSpec - Functional Specification
http://funspec.med.utoronto.ca
Functional annotation of yeast genes: GO, domains, pathways, localization, protein-interactions, etc.
100
56g:Profiler
http://biit.cs.ut.ee/gprofiler
Functional profiling: interactions, gene expression, GO, pathways, diseases, etc.
100
57G2D - Genes2Diseases
http://g2d2.ogic.ca/
Functional analysis focused on genes' inherited disease relationships including GO, protein-interactions and literature
100
58Gaggle
http://gaggle.systemsbiology.net
Integrated tools for functional analysis: gene expression, protein-interactions, pathways, etc.
100
59GARBAN - 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)
60GATHER - 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
61Gazer - 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)
62GEMS - Gene Expression Metasignatures
http://www.nursa.org/gems
A search engine to query the meta-analysis results
100
63GEM-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
64GenAge - 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
65Genapha - genomic applications for humanity
http://genapha.icapture.ubc.ca
Functional analysis tool for allergy and asthma research: pathways, SNPs and GO
100
66GenCLiP - 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
67Gendoo - Gene, Disease Features Ontology-based Overview System
http://gendoo.dbcls.jp
Functional relationships: diseases, drugs, biological phenomena
100
68Gene3D - Structure Assigned to Genomes
http://gene3d.biochem.ucl.ac.uk
A resource to explore protein domains, families, structures and protein-interactions
100
69GeneAnswers - 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
70GeneBrowser
http://orbit.nlm.nih.gov/resource/genebrowser
Identify common biological characteristics: GO, pathways, protein-interactions, gene expression, genomic elements, literature, etc.
100
71GeneCoDis - 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
72GeneDistiller
http://www.genedistiller.org
Gene prioritization based on multiple factors: GO, pathways, diseases, expression, interactions, domains, localization, etc.
100
73GeneNet - 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
74GenePattern
http://www.broadinstitute.org/cancer/software/genepattern
Integrated analysis tools: differential expression, class prediction, pathways, etc.
100
75GenePro
http://wodaklab.org/genepro
Plugin for deriving functional modules: GO, localization, evolutionary conservation, gene/protein-interactions, mRNA expression, etc.
100
76GeneRank
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)
77GeneRanker
http://cbioc.eas.asu.edu/generanker  http://www.generanker.org 
Identify and annotate gene-disease relationships by mining the biomedical literature
100
78Genes2Fans
http://actin.pharm.mssm.edu/genes2FANs
Functional association networks: protein-interactions, pathways, miRNAs, phenotypes, domains, metabolites, etc.
100
79GeneTrail
http://genetrail.bioinf.uni-sb.de
Gene set analysis: GSEA, pathways, over-representation, GO, etc.
100
80GeneXplain
http://www.genexplain.com
Unified access to a broad range of bioinformatics tools
100
81GenMAPP - 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
82Genome Network Platform
http://genomenetwork.nig.ac.jp/index_e.html
Genome, transcription factors/binding sites, and protein-interactions
100
83Genomics 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
84GenSensor Suite
http://bio.ccs.miami.edu/cgi-bin/GSS/Documentation.cgi
Functional associations: over-representation, GO, protein-interactions, PubMed
100
85GenTrepid
http://www.gentrepid.org
Gene prioritization based on pathways and disease relationships, including protein-interactions, domains and structures
100
86GEPAT - 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
87GESBAP - GEne Set Based Analysis of Polymorphisms
http://bioinfo.cipf.es/gesbap
Gene or SNP data functional analysis: GO, pathways, genetic/protein-interactions
100
88GFINDer - 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)
89GOAPhAR - Gene Ontology, Annotations and Pathways for Array Research
http://bioinformatics.kumc.edu/goaphar
Functional annotation: gene/protein annotations, protein-interactions, pathways and GO
100
90GoCat - Gene Ontology Categorizer
http://eagl.unige.ch/GOCat/
A tool for categorization of multiple genes based on GO and SwissProt keywords
100
91godisease
http://www.godisease.com
Gene associations: diseases, GO, protein-isoforms, etc.., and user keywords
100
92GOFFA
http://edkb.fda.gov/webstart/arraytrack/
GO based functional analysis of genomic and proteomic data
100
93GPSy
http://gpsy.genouest.org
Gene function prediction of conserved developmental processes by a cross-species prioritization system
100
94GRAMENE
http://www.gramene.org
An information resource and multiple analysis system for grass genomics
100
95GRANITE - 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)
96Graphle
http://sonorus.princeton.edu/graphle
Biological network creation based on functional annotation: GO, protein-interactions, etc.
100
97GraphWeb
http://biit.cs.ut.ee/graphweb
Graph-based analysis of biological networks: GO, protein-interactions, pathways, motifs, orthology, etc.
100
98GSA - Gene Set Analysis
http://www-stat.stanford.edu/~tibs/GSA
An R package for the functional analysis based on gene expression and pathways
100
99GSEA - Gene Set Enrichment Analysis
http://www.broadinstitute.org/gsea
A platform to define genes statistically significant between two groups
100
100G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools
http://bioinformatics.clemson.edu/G-SESAME
Functional similarity between genes or GO terms
100
101GVIZ - 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
102Hanalyzer - high-throughput analyzer
http://hanalyzer.sourceforge.net
Integrated functional analysis: GO, pathways, protein-interactions, domains, literature co-occurrence, etc.
100
103HEAT - 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
104KOBAS - KEGG Orthology Based Annotation System
http://kobas.cbi.pku.edu.cn/home.do
Annotation and identification of statistically enriched pathways and diseases
100
105L2L
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
106l2n - 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
107LIBGS - 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
108MAGIA - 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
109MassNet
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)
110MAVEN - 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
111MEDIE
http://www.nactem.ac.uk/tsujii/medie
Biomedical correlations from literature
100
112MEM - 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
113MetaGP - 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)
114MetaRanker
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
115MILANO - 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
116NetAtlas
http://netatlas.sourceforge.net
A Cytoscape plugin for network analysis using gene expression data: tissue-defined networks, correlated expression, cell-signaling, etc.
100
117Netview
http://netview.tigem.it
A tool to explore gene regulatory networks, including GO prediction and gene signature analysis
100
118NW - NetWalker
https://netwalkersuite.org
A network analysis tool: data normalization, clustering, protein-interactions, GO, etc.
100
119PaLS - Pathway and Literature Strainer
http://pals.bioinfo.cnio.es
Find common biological annotations: PubMed references, GO and pathways
100
120PANTHER - 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
121PathCluster
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)
122PathEx
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
123PathMAPA -
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
124Pathvar - Microarray analysis of pathway expression variance
http://pathvar.embl.de
Functional annotation: GO, pathways, protein-interaction and domains
100
125PathwayLinker
http://pathwaylinker.org
Interactions and associated signaling pathways for a given set of genes, with links to other resources
100
126PINTA - Gene Prioritization by Network Analysis
http://www.esat.kuleuven.be/pinta
Gene prioritization based on differential expression and gene/protein-interaction networks
100
127Plant 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
128PolyMAPr - 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)
129PosMed
http://omicspace.riken.jp/PosMed
Genes prioritization with an artificial neural network, and gene ranking based on biomolecular interactions and disease associations
100
130Prioritizer - 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)
131ProbFAST - Probabilistic Functional Analysis System Tool
http://gdm.fmrp.usp.br/probfast
Gene expression analysis with functional annotation including GO and pathways
100
132ProcessDB
http://www.integrativebioinformatics.com/processdb.html
A tool for modeling biological systems
100
133ProDiGe - 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
134RACE - Remote Analysis Computation for gene Expression data
http://race.unil.ch
Microarray data annotation: pre-processing, differential expression and GO
100
135SAFE - 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
136SEGS - Search for Enriched Gene Sets
http://kt.ijs.si/software/SEGS
Microarray data annotation: differential expression, GO, pathways, genetic interactions, etc.
100
137SIGNATURE - 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
138STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
http://string-db.org
Protein interaction resource with multiple annotations and functional analyses: pathways, GO, domains, and interaction-activity and clustering
100
139Suspects - Candidate gene search
http://www.genetics.med.ed.ac.uk/suspects
Candidate gene prioritization based on ranking of multiple factors: phenotypes, neighbor genes, GO, domains, gene expression, sequences and chromosomal location
100
140TAFFEL - 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
141TargetMine - 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
142Taverna
http://www.taverna.org.uk
A suite to create, edit, and execute workflows with multiple analysis: pathways, sequences, etc.
100
143TOM - 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)
144ToppCluster
http://toppcluster.cchmc.org
Feature enrichment analysis for multiple genes
100
145ToppGene Suite
http://toppgene.cchmc.org/
Gene set enrichment analysis: miRNAs, GO, protein-interactions, pathways, pharmacome, literature co-citations, transcription factors/binding sites, etc.
100
146T-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)
147TS-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
148VAVIEN - 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)
149VisANT - 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
150VISTA
http://genome.lbl.gov/vista/index.shtml
A suite for comparative analysis of genomic sequences
100
151WebGestalt - WEB-based GEne SeT AnaLysis Toolkit
http://bioinfo.vanderbilt.edu/webgestalt
Gene set analysis: GO, pathways, gene expression, etc.
100
152WebGimm - Cluster Analysis Server
http://www.eh3.uc.edu/gimm/webgimm
Clustering and functional enrichment of microarray data including pre-processing
100
153WhichGenes
http://www.whichgenes.org
Gene set creation and comparison based on biological annotations
100
copyright © Dr. Kshitish Acharya K; all rights reserved

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