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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GORetriever Resource Report Resource Website 10+ mentions |
GORetriever (RRID:SCR_005633) | GORetriever | analysis service resource, data analysis service, production service resource, service resource | GORetriever is used to find all of the GO annotations corresponding to a list of user-supplied protein identifiers. GORetriever produces a list of proteins and their annotations and a separate list of entries with no GO annotation. Platform: Online tool | gene, annotation, protein, ontology or annotation search engine |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149140 | SCR_005633 | AgBase GORetriever | 2026-09-05 06:31:30 | 13 | |||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-09-05 06:31:31 | 36 | |||||
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MetaGeneProfiler Resource Report Resource Website |
MetaGeneProfiler (RRID:SCR_005794) | MetaGP | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Meta Gene Profiler (MetaGP) is a web application tool for discovering differentially expressed gene sets (meta genes) from the gene set library registered in our database. Once user submits gene expression profiles which are categorized into subtypes of conditioned experiments, or a list of genes with the valid pvalues, MetaGP assigns the integrated p-value to each gene set by combining the statistical evidences of genes that are obtained from gene-level analysis of significance. The current version supports the nine Affymetrix GeneChip arrays for the three organisms (human, mouse and rat). The significances of GO terms are graphically mapped onto the directed acyclic graph (DAG). The navigation systems of GO hierarchy enable us to summarize the significance of interesting sub-graphs on the web browser. Platform: Online tool | gene, gene expression, differentially expressed, gene ontology, meta gene, gene set, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Institute of Statistical Mathematics; Tokyo; Japan |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149271 | SCR_005794 | Meta Gene Profiler, MetaGeneProfiler on the WEB, Meta Gene Profiler (MetaGP), MetaGeneProfiler on the WEB - Web service for significance test of differentially-expressed Meta Genes | 2026-09-05 06:31:31 | 0 | |||||||
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OntoVisT Resource Report Resource Website 1+ mentions |
OntoVisT (RRID:SCR_005674) | OntoVisT | data or information resource, database, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. Web based ontological visualization tool for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery. | ontology, visualization, web service, gene ontology, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, dag hierarchical form, dag, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: OBO has parent organization: Jawaharlal Nehru University; New Delhi; India |
Council of Scientific and Industrial Research; New Delhi; India ; Jawaharlal Nehru University; New Delhi; India ; Department of Biotechnology |
PMID:21738333 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02274, nlx_149113 | SCR_005674 | OntoVisT: A General purpose Ontological Visualization Tool | 2026-09-05 06:31:31 | 1 | |||||
|
OntoGate Resource Report Resource Website |
OntoGate (RRID:SCR_005795) | OntoGate | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2012. OntoGate provides access to GenomeMatrix (GM) entries from Ontology terms and external datasets which have been associated with ontology terms, to find genes from different species in the GM, which have been mapped to the ontology terms. OntoGate includes a BLAST search of amino acid sequences corresponding to annotated genes. Platform: Online tool | gene, ontology, blast, amino acid sequence, annotation, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
PMID:12824422 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149274 | SCR_005795 | 2026-09-05 06:31:31 | 0 | |||||||
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WEGO - Web Gene Ontology Annotation Plot Resource Report Resource Website 100+ mentions |
WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) | WEGO | analysis service resource, data analysis service, production service resource, service resource | Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool | visualization, gene ontology, gene, annotation, comparative genomics, histogram, directed acyclic graph, genomics, genome, ontology or annotation visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: BGI; Shenzhen; China |
Zhejiang University ; Chinese Academy of Sciences ; Danish Basic Research Foundation ; Ministry of Science and Technology 2002AA104250; Ministry of Science and Technology CNGI-04-15-7A; National Natural Science Foundation of China 30399120; National Natural Science Foundation of China 90208019; National Natural Science Foundation of China 30200163; National Natural Science Foundation of China 90403130 |
PMID:16845012 | Free for academic use | biotools:wego, nlx_149334 | https://bio.tools/wego | SCR_005827 | BGI WEGO - Web Gene Ontology Annotation Plotting, Web Gene Ontology Annotation Plot | 2026-09-05 06:31:32 | 398 | ||||
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REViGO Resource Report Resource Website 1000+ mentions |
REViGO (RRID:SCR_005825) | REViGO | analysis service resource, data analysis service, production service resource, service resource | Web server that summarizes lists of Gene Ontology terms by removing redundant terms and visualizing the remaining ones in scatterplots, interactive graphs, treemaps, or tag clouds. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene ontology, visualization, statistical analysis, ontology or annotation visualization |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Rudjer Boskovic Institute; Zagreb; Croatia |
PMID:21789182 PMID:20585573 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02283, nlx_149332 | SCR_005825 | Reduce + Visualize Gene Ontology, REViGO - Reduce Visualize Gene Ontology, REViGO - Reduce & Visualize Gene Ontology, REViGO - Reduce and Visualize Gene Ontology, REViGO - Reduce + Visualize Gene Ontology | 2026-09-05 06:31:32 | 2430 | ||||||
|
Network Ontology Analysis Resource Report Resource Website 1+ mentions |
Network Ontology Analysis (RRID:SCR_005667) | NOA | analysis service resource, data analysis service, production service resource, service resource | Network Ontology Analysis (NOA) (abbreviated to NOA) is a freely available collection of Gene Ontology tools aiming to analyze functions of gene network instead of gene list. Network rewiring facilitates the function changes between conditions even with the same gene list. Therefore, it is necessary to annotate the specific function of networks by considering the fundamental roles of interactions from the viewpoint of systems biology. NOA is such a novel functional enrichment analysis method capable to handle both dynamic and static networks. The application of NOA in biological networks shows that NOA can not only capture changing functions in rewiring networks but also find more relevant and specific functions in traditional static networks. Platform: Online tool | gene, ontology, ontology or annotation browser, statistical analysis, term enrichment, browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Chinese Academy of Sciences; Beijing; China |
Chief Scientist Program of SIBS 2009CSP002; Knowledge Innovation Program of CAS KSCX2-EW-R-01; NSFC 61072149; NSFC 91029301; NSFC 60873205; NSFC 10801131; NSFC 60970091; Shanghai NSF 11ZR1443100 |
PMID:21543451 | Open unspecified license - Free for academic use | nlx_149105 | SCR_005667 | Network Ontology Analysis (NOA) | 2026-09-05 06:31:31 | 7 | |||||
|
SNPsandGO Resource Report Resource Website 50+ mentions |
SNPsandGO (RRID:SCR_005788) | SNPs&GO | analysis service resource, data analysis service, production service resource, service resource | A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans. | prediction, protein, mutation, disease, single nucleotide polymorphism, bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Bologna; Bologna; Italy |
PMID:19514061 | biotools:snps_go, OMICS_02219 | https://bio.tools/snps_go | SCR_005788 | SNPs and GO | 2026-09-05 06:31:31 | 61 | ||||||
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OBO-Edit Resource Report Resource Website 10+ mentions |
OBO-Edit (RRID:SCR_005668) | OBO-Edit | software application, software resource, source code | OBO-Edit is an open source, platform-independent application written in Java for viewing and editing any OBO format ontologies. OBO-Edit is a graph-based tool; its emphasis on the overall graph structure of an ontology provides a friendly interface for biologists, and makes OBO-Edit excellent for the rapid generation of large ontologies focusing on relationships between relatively simple classes. The UI components are cleanly separated from the data model and data adapters, so these can be reused in other applications. The oboedit foward-chaining reasoner can also be used independently (for example, for traversing ontology graphs). OBO-Edit uses the OBO format flat file. See the GO wiki, http://wiki.geneontology.org/index.php/OBO-Edit:_Getting_the_Source_Code, for instructions on downloading the source code. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, browser, search engine, visualization, editor, software library, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: OBO is related to: Ontology Lookup Service is related to: Phenote: A Phenotype Annotation Tool using Ontologies has parent organization: Gene Ontology |
PMID:17545183 | Open unspecified license - Free for academic use | nlx_149107 | http://org.geneontology.oboedit | SCR_005668 | OBO-Edit: The OBO Ontology Editor | 2026-09-05 06:31:31 | 21 | |||||
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Yeast Search for Transcriptional Regulators And Consensus Tracking Resource Report Resource Website 100+ mentions |
Yeast Search for Transcriptional Regulators And Consensus Tracking (RRID:SCR_006076) | YEASTRACT | data or information resource, database | A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database. | yeast, gene, regulatory association, transcription factor, target gene, genomic, transcription regulation, transcription, web service, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SGD is related to: Gene Ontology is related to: Regulatory Sequence Analysis Tools |
Fundacao para a Ciencia e a Tecnologia contract Pest-OE/EQB/LA0023/2011_research line: Systems and Synthetic Biology; Fundacao para a Ciencia e a Tecnologia ERA-IB/0002/2010; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-EIA/111239/2009; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-CCO/118522/2010 |
PMID:24170807 PMID:20972212 PMID:18032429 PMID:16381908 |
Free | nif-0000-03652, OMICS_00547, biotools:yeastract | https://bio.tools/yeastract | SCR_006076 | 2026-09-05 06:31:33 | 130 | |||||
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G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools Resource Report Resource Website 1+ mentions |
G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools (RRID:SCR_005816) | G-SESAME | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2,2025. G-SESAME contains a set of tools. They include: tools for measuring the semantic similarity of GO terms; tools for measuring the functional similarity of genes; and tools for clustering genes based on their GO term annotation information. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene ontology, semantic similarity, functional similarity, cluster, gene, annotation, gene annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Clemson University; South Carolina; USA |
NSF DBI-0960586; NSF DBI-0960443 |
PMID:19491312 PMID:17344234 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149313 | SCR_005816 | Gene Semantic Similarity Analysis Measurement Tools, Gene Semantic Similarity Analysis and Measurement Tools | 2026-09-05 06:31:32 | 5 | |||||
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MalaCards Resource Report Resource Website 100+ mentions |
MalaCards (RRID:SCR_005817) | MalaCards | data or information resource, database | An integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. The database contains 17,705 diseases, consolidated from 28 sources. | malady, annotation, gene, disease, cellular component, biological process, molecular function, expression profile, pathway, drug, compound, publication, phenotype, ortholog, gene ontology, FASEB list |
is related to: Gene Ontology is related to: Mouse Genome Informatics (MGI) is related to: DrugBank is related to: KEGG is related to: OMIM is related to: PharmGKB is related to: National Institute of Neurological Disorders and Stroke is related to: Office of Rare Diseases Research is related to: Bookshelf is related to: MedlinePlus is related to: Centers for Disease Control and Prevention |
nlx_149314, r3d100012018 | https://doi.org/10.17616/R30W7D | SCR_005817 | MalaCards - The Human Malady Compendium | 2026-09-05 06:31:32 | 424 | |||||||
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TXTGate Resource Report Resource Website |
TXTGate (RRID:SCR_005812) | TXTGate | analysis service resource, data analysis service, production service resource, service resource | TXTGate is a literature index database and is part of an experimental platform to evaluate (combinations of) information extraction and indexing from a variety of biological annotation databases. It is designed towards the summarization and analysis of groups of genes based on text. By means of tailored vocabularies, selected textual fields and MedLine abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles. You need to be registered in order to use the TXTGate application. Platform: Online tool | gene, annotation, database, text mining |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: SGD has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium |
European Union ; Instituut voor de aanmoediging van Innovatie door Wetenschap en Technologie Vlaanderen ; Research Council K.U. Leuven GOA-Mefisto-666; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0115.01; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0240.99; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0407.02; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0413.03; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0388.03; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0229.03; Fonds voor Wetenschappelijk Onderzoek - Vlaanderen G.0241.04; Belgian Federal Science Policy Office IUAP V-22 |
PMID:15186494 | Free for academic use | nlx_149305 | SCR_005812 | 2026-09-05 06:31:32 | 0 | ||||||
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IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures Resource Report Resource Website 1+ mentions |
IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures (RRID:SCR_005815) | IT-GOM | analysis service resource, data analysis service, production service resource, service resource | The Integrated Tool for IC-based GO Semantic Similarity Measures (IT-GOM) integrates the currently known GO semantic similarity measures into a single tool. It provides the information content (IC) of GO terms, semantic similarity between GO terms and GO-based protein functional similarity scores. The specificity of GO terms and the similarity of biological content between GO terms or proteins are transformed into numeric values for protein analyses at the functional level. The integration of the different measures enables users to choose the measure best suited to their application and to compare results between different semantic similarity measures. Platform: Online tool | semantic similarity, gene ontology, protein, functional similarity, function, annotation, topology |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: GOA has parent organization: University of Cape Town; Western Cape; South Africa |
National Bioinformatics Network in South Africa ; University of Cape Town; Western Cape; South Africa ; Computational Biology research group at the Institute of Infectious Disease and Molecular Medicine |
Open unspecified license - Free for academic use | nlx_149310 | SCR_005815 | Integrated Tool for IC-based GO Semantic Similarity Measures (IT-GOM), Integrated Tool for IC-based GO Semantic Similarity Measures | 2026-09-05 06:31:32 | 1 | ||||||
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CharProtDB: Characterized Protein Database Resource Report Resource Website |
CharProtDB: Characterized Protein Database (RRID:SCR_005872) | CharProtDB | data or information resource, database | The Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ��synonymous accessions��. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated. | protein, annotation, functional annotation, taxonomic classification, literature, gene ontology, evidence code, enzyme commission, transport classification, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute |
NHGRI R01 HG004881; NIAID contract HHSN266200100038C |
PMID:22140108 | biotools:charprotdb, nlx_149421 | https://bio.tools/charprotdb | SCR_005872 | Characterized Protein Database | 2026-09-05 06:31:32 | 0 | |||||
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CLASSIFI - Cluster Assignment for Biological Inference Resource Report Resource Website |
CLASSIFI - Cluster Assignment for Biological Inference (RRID:SCR_005752) | CLASSIFI | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 10, 2012. Cluster Assignment for Biological Inference (CLASSIFI) is a data-mining tool that can be used to identify significant co-clustering of genes with similar functional properties (e.g. cellular response to DNA damage). Briefly, CLASSIFI uses the Gene Ontology gene annotation scheme to define the functional properties of all genes/probes in a microarray data set, and then applies a cumulative hypergeometric distribution analysis to determine if any statistically significant gene ontology co-clustering has occurred. Platform: Online tool | statistical analysis, gene, gene expression, data mining, biological process, function, gene ontology, annotation, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: UT Southwestern Medical Center Department of Pathology |
PMID:16670020 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149214 | SCR_005752 | Cluster Assignment for Biological Inference, Cluster Assignment for Biological Inference (CLASSIFI) | 2026-09-05 06:31:31 | 0 | ||||||
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GraphWeb Resource Report Resource Website 10+ mentions |
GraphWeb (RRID:SCR_005746) | GraphWeb | analysis service resource, data analysis service, production service resource, service resource | GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online tool | analysis, biological network, ontology or annotation visualization, protein interaction, gene id conversion, orthology mapping, network visualization, graph clustering, gene ontology, cis-regulatory motif, module, network, pathway, biological pathway, motif, visualization, protein interaction, orthology mapping, network visualization, graph clustering, analysis, statistical analysis, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group |
European Union FP6 ENFIN LSHG-CT-2005-518254; European Union FP6 COBRED LSHB-CT-2007-037730; Estonian Science Foundation ETF7437 |
PMID:18460544 | Open unspecified license - Free for academic use | nlx_149205 | SCR_005746 | 2026-09-05 06:31:31 | 12 | ||||||
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ProteInOn Resource Report Resource Website 1+ mentions |
ProteInOn (RRID:SCR_005740) | analysis service resource, data analysis service, production service resource, service resource | ProteInOn calculates semantic similarity between GO terms or proteins annotated with GO terms. It also calculates term enrichment of protein sets, by applying a term representativity score, and gives additional information on protein interactions. The query compute protein semantic similarity returns the semantic similarity scores between all proteins entered, in matrix format. The option Measure allows users to choose one of several semantic similarity measures: Resnik, Lin, or Jiang & Conrath's measures with or without the DCA approach, plus the graph-based simUI and simGIC measures. These measures are listed by order of performance as evaluated with protein sequence similarity. The option GO type allows users to choose one of the aspects of GO: molecular function, biological process and cellular component. The option Ignore IEA limits the query to non-electronic annotations, excluding evidence types: IEA, NAS, ND, NR. | protein, ontology, gene ontology, annotation, statistical analysis, term enrichment, protein interaction, semantic similarity, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products has parent organization: University of Lisbon; Lisbon; Portugal |
Free for academic use | nlx_149206 | SCR_005740 | Protein Interactions Ontology, ProteInOn - Protein Interactions and Ontology, Protein Interactions and Ontology | 2026-09-05 06:31:31 | 2 | ||||||||
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VirHostNet: Virus-Host Network Resource Report Resource Website 1+ mentions |
VirHostNet: Virus-Host Network (RRID:SCR_005978) | VirHostNet | data or information resource, database | Public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. It contains high quality and up-to-date information gathered and curated from public databases (VirusMint, Intact, HIV-1 database). It allows users to search by host gene, host/viral protein, gene ontology function, KEGG pathway, Interpro domain, and publication information. It also allows users to browse viral taxonomy. | interaction, protein, virus, protein-protein interaction, protein interaction, infectious disease, antiviral drug design, proteome, interactome, molecular function, cellular pathway, protein domain, virus-virus, virus-host, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: VirusMINT is related to: IntAct is related to: HIV-1 Human Protein Interaction Database is related to: PSICQUIC Registry has parent organization: Claude Bernard University Lyon 1; Lyon; France |
PMID:18984613 | Acknowledgement requested, Public | nif-0000-03634, OMICS_01910, biotools:virhostnet | https://bio.tools/virhostnet | SCR_005978 | Virus-Host Network | 2026-09-05 06:31:32 | 7 |
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