1 | ASSESS - Analysis of Sample Set Enrichment Scores http://people.genome.duke.edu/assess | Functional annotation and statistical analysis across phenotypes: pathways, motifs and cytogenetics |
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2 | 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. |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
3 | 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 |
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4 | GENEMANIA http://www.genemania.org | Functional association networks: GO terms, co-expression, domains, pathways, co-localization and genetic/protein-interactions |
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5 | 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 |
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6 | Blast2GO http://www.blast2go.com | Functional annotation of sequences (novel and annotated): GO, pathways, and various visualizations |
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7 | CGI http://www-rcf.usc.edu/~fsun/Programs/CGI/CGIMain.html | Gene prioritization based on gene expression and protein-interactions |
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8 | CLEAN - CLustering Enrichment ANalysis http://eh3.uc.edu/clean | Clustering and calculation of gene specific functional coherence scores to microarray data |
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9 | BioLayout Express3D http://www.biolayout.org | Gene networks based on relationships: disease, protein-interactions, pathways, gene expression, sequence similarity, regulatory cascades, etc. |
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10 | AgBase http://www.agbase.msstate.edu | Integrated tools for functional analysis of agricultural plant and animal gene products |
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11 | 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. |
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12 | ArrayXPath http://www.snubi.org/software/ArrayXPath | Functional analysis of gene expression data: GO, pathways, disease, etc. |
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13 | 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. |
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14 | BioProfiling.de http://www.bioprofiling.de | Integrated analysis of gene lists: GO, protein interactions, miRNAs, pathways, GWAS, metabolomics, etc. |
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15 | ADGO http://www.btool.org/ADGO2 | Microarray data annotation: GO, pathways, transcription factor binding sites, miRNA, etc. |
| | URL not working as on 18 Jan 2014 (confirmed on 3 Nov 2016) |
16 | 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. |
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17 | AMEN - Annotation, Mapping, Expression and Network http://amen.sourceforge.net | Functional annotation: protein-interaction, chromosomal location and expression |
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18 | ArrayProspector http://www.bork.embl.de/ArrayProspector | Functional analysis of gene expression data: co-expression, protein-interactions and pathways |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
19 | ArrayWiki http://arraywiki.bme.gatech.edu | A platform for sharing microarray data repositories and meta-analysis |
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20 | atBioNet http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm | Gene network analysis: protein-interactions and pathways |
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21 | BIANA - Biologic Interactions and Network Analysis http://sbi.imim.es/web/BIANA.php | Functional annotation: functions, pathways, protein-interactions, etc. |
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22 | 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 |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
23 | BiologicalNetworks/IntegromeDB/PathSys http://biologicalnetworks.net | Integrated functional analysis: gene/protein-interactions, pathways, transcriptional regulation, GO, promoter analysis, diseases, structures, etc. |
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24 | BioNetBuilder http://err.bio.nyu.edu/cytoscape/bionetbuilder | A Cytoscape plugin for creation of biological networks: GO, protein-interactions, pathways, domains, etc. |
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25 | BIOZON http://www.biozon.org | Unified biological resource for integrated analysis: GO, pathways, protein-interactions, domains, gene expression, etc. |
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26 | BITOLA - Biomedical Discovery Support System http://ibmi.mf.uni-lj.si/bitola | Literature based biological associations: disease, tissue, pathology, pathway, drug, etc. |
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27 | CancerResource http://bioinf-data.charite.de/cancerresource | Functional annotation focused on cancer: GO, pathways, gene expression, drugs, protein-interactions, structures, etc. |
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28 | 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. |
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29 | CARMAweb https://carmaweb.genome.tugraz.at/carma | Microarray data annotation: pre-processing, differential expression, clustering and GO |
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30 | Chilibot - Mining PubMed for relationships http://www.chilibot.net | Find relationships between proteins/genes/keywords by searching PubMed |
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31 | ClueGO http://www.ici.upmc.fr/cluego | A Cytoscape plugin to visualize biological terms for a given set of genes in a functional network |
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32 | cmap - Connectivity Map http://www.broadinstitute.org/cmap | Find connections between biological entities: expression profiles, drug and gene interactions, diseases, etc. |
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33 | 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 |
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34 | ConceptGen http://conceptgen.ncibi.org/ | Enrichment testing and concept mapping tool |
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35 | 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 |
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36 | 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. |
| | URL not working as on 3 Nov 2016 |
37 | CORNET - CORrelation NETworks https://bioinformatics.psb.ugent.be/cornet | Functional annotation of Arabidopsis genes: co-expression, transcription regulation, protein-interactions, GO, pathways, etc. |
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38 | 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 |
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39 | DEEP - Differential Expression Effector Prediction http://deep.bioinf.med.uni-goettingen.de | Differential expression with signaling networks |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
40 | DIR http://cbc.case.edu/dir | Functional relationships of disease genes vs. candidate genes: protein-interaction, gene expression, pathway, etc. |
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41 | DiscoverySpace http://www.bcgsc.ca/platform/bioinfo/software/ds | A platform for high-throughput data analysis |
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42 | 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. |
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43 | DRAGON - Database Referencing of Array Genes ONline http://pevsnerlab.kennedykrieger.org/dragon.htm | Integrated functional analysis: gene expression, localization, domains, function, pathways, etc. |
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44 | DTFAM - Dragon TF Association Miner http://research.i2r.a-star.edu.sg/DRAGON/TFAM | Functional associations: literature keywords, GO, diseases, transcription factors, etc. |
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45 | Find relationships (informative terms: iTerms) for gene(s) from literature |
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46 | Endeavour http://www.esat.kuleuven.be/endeavour | Gene prioritization based on multiple factors: protein-interactions, gene expression, transcriptional regulation, localization, pathways, GO, literature, etc. |
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47 | Enrichment Map http://baderlab.org/Software/EnrichmentMap | Plugin for functional enrichment and visualizations: GSEA, GO, pathways, etc. |
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48 | ERGO Genome Analysis & Discovery System https://ergo.integratedgenomics.com | Systems biology platform for analysis of organisms with many integrated tools |
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49 | ermineJ http://www.chibi.ubc.ca/ermineJ | Gene set analysis tool: ranking, over-representation, GO, etc. |
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50 | 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. |
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51 | 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. |
| | URL not working as on 20 Jan 2014; getting error 403 (confirmed on 3 Nov 2016) |
52 | 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. |
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53 | FunCoup - Networks of functional coupling http://FunCoup.sbc.su.se | Functional relationships: gene expression, interaction, localization, etc. |
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54 | FunNet - Transcriptional Networks Analysis http://www.funnet.info | Transcriptional interactions and co-expression analysis of gene expression data |
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55 | FunSpec - Functional Specification http://funspec.med.utoronto.ca | Functional annotation of yeast genes: GO, domains, pathways, localization, protein-interactions, etc. |
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56 | g:Profiler http://biit.cs.ut.ee/gprofiler | Functional profiling: interactions, gene expression, GO, pathways, diseases, etc. |
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57 | G2D - Genes2Diseases http://g2d2.ogic.ca/ | Functional analysis focused on genes' inherited disease relationships including GO, protein-interactions and literature |
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58 | Gaggle http://gaggle.systemsbiology.net | Integrated tools for functional analysis: gene expression, protein-interactions, pathways, etc. |
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59 | GARBAN - Genomic Analysis and Rapid Biological Annotation http://garban.tecnun.es | Functional classification of genes: differential expression, GO, pathways, etc. |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
60 | 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. |
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61 | Gazer - Gene Set Analyzer http://integromics.kobic.re.kr/Gazer | Microarray data annotation: GO, pathways, domain, etc. |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
62 | GEMS - Gene Expression Metasignatures http://www.nursa.org/gems | A search engine to query the meta-analysis results |
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63 | 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 |
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64 | 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. |
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65 | Genapha - genomic applications for humanity http://genapha.icapture.ubc.ca | Functional analysis tool for allergy and asthma research: pathways, SNPs and GO |
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66 | 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 |
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67 | Gendoo - Gene, Disease Features Ontology-based Overview System http://gendoo.dbcls.jp | Functional relationships: diseases, drugs, biological phenomena |
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68 | Gene3D - Structure Assigned to Genomes http://gene3d.biochem.ucl.ac.uk | A resource to explore protein domains, families, structures and protein-interactions |
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69 | 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. |
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70 | GeneBrowser http://orbit.nlm.nih.gov/resource/genebrowser | Identify common biological characteristics: GO, pathways, protein-interactions, gene expression, genomic elements, literature, etc. |
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71 | 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. |
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72 | GeneDistiller http://www.genedistiller.org | Gene prioritization based on multiple factors: GO, pathways, diseases, expression, interactions, domains, localization, etc. |
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73 | 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 |
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74 | GenePattern http://www.broadinstitute.org/cancer/software/genepattern | Integrated analysis tools: differential expression, class prediction, pathways, etc. |
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75 | GenePro http://wodaklab.org/genepro | Plugin for deriving functional modules: GO, localization, evolutionary conservation, gene/protein-interactions, mRNA expression, etc. |
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76 | GeneRank http://bodymap.ims.u-tokyo.ac.jp/ | Gene prioritization based on gene expression and GO annotations |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
77 | GeneRanker http://cbioc.eas.asu.edu/generanker http://www.generanker.org | Identify and annotate gene-disease relationships by mining the biomedical literature |
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78 | Genes2Fans http://actin.pharm.mssm.edu/genes2FANs | Functional association networks: protein-interactions, pathways, miRNAs, phenotypes, domains, metabolites, etc. |
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79 | GeneTrail http://genetrail.bioinf.uni-sb.de | Gene set analysis: GSEA, pathways, over-representation, GO, etc. |
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80 | GeneXplain http://www.genexplain.com | Unified access to a broad range of bioinformatics tools |
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81 | 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 |
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82 | Genome Network Platform http://genomenetwork.nig.ac.jp/index_e.html | Genome, transcription factors/binding sites, and protein-interactions |
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83 | 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. |
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84 | GenSensor Suite http://bio.ccs.miami.edu/cgi-bin/GSS/Documentation.cgi | Functional associations: over-representation, GO, protein-interactions, PubMed |
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85 | GenTrepid http://www.gentrepid.org | Gene prioritization based on pathways and disease relationships, including protein-interactions, domains and structures |
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86 | 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 |
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87 | GESBAP - GEne Set Based Analysis of Polymorphisms http://bioinfo.cipf.es/gesbap | Gene or SNP data functional analysis: GO, pathways, genetic/protein-interactions |
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88 | GFINDer - Genome Function INtegrated Discoverer http://www.medinfopoli.polimi.it/GFINDer | Functional annotation: GO, pathways, protein-interaction, genetic disorders, domains, etc., including statistical analysis |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
89 | GOAPhAR - Gene Ontology, Annotations and Pathways for Array Research http://bioinformatics.kumc.edu/goaphar | Functional annotation: gene/protein annotations, protein-interactions, pathways and GO |
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90 | GoCat - Gene Ontology Categorizer http://eagl.unige.ch/GOCat/ | A tool for categorization of multiple genes based on GO and SwissProt keywords |
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91 | godisease http://www.godisease.com | Gene associations: diseases, GO, protein-isoforms, etc.., and user keywords |
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92 | GOFFA http://edkb.fda.gov/webstart/arraytrack/ | GO based functional analysis of genomic and proteomic data |
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93 | GPSy http://gpsy.genouest.org | Gene function prediction of conserved developmental processes by a cross-species prioritization system |
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94 | GRAMENE http://www.gramene.org | An information resource and multiple analysis system for grass genomics |
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95 | 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. |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
96 | Graphle http://sonorus.princeton.edu/graphle | Biological network creation based on functional annotation: GO, protein-interactions, etc. |
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97 | GraphWeb http://biit.cs.ut.ee/graphweb | Graph-based analysis of biological networks: GO, protein-interactions, pathways, motifs, orthology, etc. |
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98 | GSA - Gene Set Analysis http://www-stat.stanford.edu/~tibs/GSA | An R package for the functional analysis based on gene expression and pathways |
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99 | GSEA - Gene Set Enrichment Analysis http://www.broadinstitute.org/gsea | A platform to define genes statistically significant between two groups |
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100 | G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools http://bioinformatics.clemson.edu/G-SESAME | Functional similarity between genes or GO terms |
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101 | 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. |
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102 | Hanalyzer - high-throughput analyzer http://hanalyzer.sourceforge.net | Integrated functional analysis: GO, pathways, protein-interactions, domains, literature co-occurrence, etc. |
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103 | 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 |
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104 | KOBAS - KEGG Orthology Based Annotation System http://kobas.cbi.pku.edu.cn/home.do | Annotation and identification of statistically enriched pathways and diseases |
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105 | 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. |
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106 | l2n - Lists2Networks http://www.lists2networks.org | Integrated functional analysis: co-expression, co-annotation, protein-interactions, GO, pathways, domains, miRNA, metabolites, etc. |
| | URL not working as on 20 Jan 2014 |
107 | 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 |
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108 | 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. |
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109 | MassNet http://massnet.kr | Functional annotation of mass-spec data: protein-interactions, physico-chemical analysis, pathways, GO, etc. |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
110 | 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. |
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111 | MEDIE http://www.nactem.ac.uk/tsujii/medie | Biomedical correlations from literature |
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112 | 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. |
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113 | MetaGP - MetaGeneProfiler http://metagp.ism.ac.jp | Differential expression and significance analysis from microarray data: GO, pathways and transcription modules |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
114 | 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. |
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115 | 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 |
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116 | NetAtlas http://netatlas.sourceforge.net | A Cytoscape plugin for network analysis using gene expression data: tissue-defined networks, correlated expression, cell-signaling, etc. |
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117 | Netview http://netview.tigem.it | A tool to explore gene regulatory networks, including GO prediction and gene signature analysis |
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118 | NW - NetWalker https://netwalkersuite.org | A network analysis tool: data normalization, clustering, protein-interactions, GO, etc. |
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119 | PaLS - Pathway and Literature Strainer http://pals.bioinfo.cnio.es | Find common biological annotations: PubMed references, GO and pathways |
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120 | 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. |
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121 | PathCluster http://www.systemsbiology.co.kr/PathCluster | Gene set clustering based on functional annotation: GO, motifs, transcription regulation, molecular-interactions |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
122 | 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. |
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123 | PathMAPA - http://bioinformatics.med.yale.edu/pathmapa.htm | Search and manipulate Arabidopsis microarray data: gene expression, enzymes, pathways eith expression overlay, statistical analysis, etc. |
| | 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 |
124 | Pathvar - Microarray analysis of pathway expression variance http://pathvar.embl.de | Functional annotation: GO, pathways, protein-interaction and domains |
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125 | PathwayLinker http://pathwaylinker.org | Interactions and associated signaling pathways for a given set of genes, with links to other resources |
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126 | PINTA - Gene Prioritization by Network Analysis http://www.esat.kuleuven.be/pinta | Gene prioritization based on differential expression and gene/protein-interaction networks |
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127 | 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 |
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128 | 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. |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
129 | PosMed http://omicspace.riken.jp/PosMed | Genes prioritization with an artificial neural network, and gene ranking based on biomolecular interactions and disease associations |
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130 | 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. |
| | URL directs to a different webpage (as on 3 Nov 2016) |
131 | ProbFAST - Probabilistic Functional Analysis System Tool http://gdm.fmrp.usp.br/probfast | Gene expression analysis with functional annotation including GO and pathways |
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132 | ProcessDB http://www.integrativebioinformatics.com/processdb.html | A tool for modeling biological systems |
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133 | 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 |
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134 | RACE - Remote Analysis Computation for gene Expression data http://race.unil.ch | Microarray data annotation: pre-processing, differential expression and GO |
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135 | 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 |
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136 | SEGS - Search for Enriched Gene Sets http://kt.ijs.si/software/SEGS | Microarray data annotation: differential expression, GO, pathways, genetic interactions, etc. |
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137 | 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 |
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138 | STRING - 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 |
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139 | Suspects - 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 |
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140 | 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 |
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141 | 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. |
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142 | Taverna http://www.taverna.org.uk | A suite to create, edit, and execute workflows with multiple analysis: pathways, sequences, etc. |
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143 | 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. |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
144 | ToppCluster http://toppcluster.cchmc.org | Feature enrichment analysis for multiple genes |
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145 | ToppGene Suite http://toppgene.cchmc.org/ | Gene set enrichment analysis: miRNAs, GO, protein-interactions, pathways, pharmacome, literature co-citations, transcription factors/binding sites, etc. |
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146 | T-Profiler http://hjbweb.bio.columbia.edu/t-profiler/index.html | Microarray data annotation: consensus motifs, transcription modules, aneuploidy and GO |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
147 | 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. |
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148 | VAVIEN - Prioritize disease genes http://www.diseasegenes.org | Candidate disease genes prioritization based on topological similarity of proteins in interaction networks |
| | URL not working as on 20 Jan 2014 (confirmed on 3 Nov 2016) |
149 | 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. |
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150 | VISTA http://genome.lbl.gov/vista/index.shtml | A suite for comparative analysis of genomic sequences |
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151 | WebGestalt - WEB-based GEne SeT AnaLysis Toolkit http://bioinfo.vanderbilt.edu/webgestalt | Gene set analysis: GO, pathways, gene expression, etc. |
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152 | WebGimm - Cluster Analysis Server http://www.eh3.uc.edu/gimm/webgimm | Clustering and functional enrichment of microarray data including pre-processing |
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153 | WhichGenes http://www.whichgenes.org | Gene set creation and comparison based on biological annotations |
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