Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GO-Module Resource Report Resource Website 1+ mentions |
GO-Module (RRID:SCR_005813) | GO-Module | production service resource, data analysis service, analysis service resource, service resource | GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool | functional similarity, visualization, other analysis, reduce the dimensionality of go enrichment results, produce interpretable biomodules of significant go terms, gene ontology, ontology or annotation visualization, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: AmiGO has parent organization: University of Illinois at Chicago; Illinois; USA |
NIH ; Cancer Research Foundation ; NLM K22 LM008308; NCI 1U54CA121852; NCRR UL1 RR024999 |
PMID:21421553 | Free for academic use | nlx_149322 | SCR_005813 | Hierarchical optimization of enriched GO terms | 2026-08-10 09:32:39 | 3 | |||||
|
GOanna Resource Report Resource Website 10+ mentions |
GOanna (RRID:SCR_005684) | GOanna | production service resource, data analysis service, analysis service resource, service resource | GOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database of GO annotated proteins. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match. Platform: Online tool | agriculture, annotation, protein, ontology or annotation search engine, ontology or annotation editor |
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_149139 | SCR_005684 | AgBase GOanna | 2026-08-10 09:32:37 | 17 | |||||
|
FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products Resource Report Resource Website |
FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products (RRID:SCR_005738) | FuSSiMeG | production service resource, data analysis service, analysis service resource, service resource | FuSSiMeG is being discontinued, may not be working properly. Please use our new tool ProteinOn. Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) provides a functional similarity measure between two proteins using the semantic similarity between the GO terms annotated with the proteins. Platform: Online tool | protein, similarity, gene ontology, gene, ontology, statistical analysis, term enrichment, semantic similarity, analysis, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: ProteInOn has parent organization: University of Lisbon; Lisbon; Portugal |
Free for academic use | nlx_149198 | SCR_005738 | Functional Semantic Similarity Measure between Gene-Products, Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) | 2026-08-10 09:32:38 | 0 | |||||||
|
Mouse Genome Informatics (MGI) Resource Report Resource Website 1000+ mentions |
Mouse Genome Informatics (MGI) (RRID:SCR_006460) | MGI | data or information resource, database | International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI. | RIN, Resource Information Network, molecular neuroanatomy resource, human health, human disease, animal model, gene expression, phenotype, genotype, gene, pathway, orthology, tumor, strain, single nucleotide polymorphism, recombinase, function, blast, image, pathology, model, data analysis service, genome, genetics, gold standard, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is used by: Cytokine Registry is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is listed by: NIH Data Sharing Repositories is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: MONARCH Initiative is related to: MouseCyc is related to: AmiGO is related to: Gene Expression Database is related to: Bgee: dataBase for Gene Expression Evolution is related to: HomoloGene is related to: Rat Gene Symbol Tracker is related to: Enhancer Trap Line Browser is related to: Integrated Brain Gene Expression is related to: MalaCards is related to: Gene Ontology is related to: BioMart Project is related to: NIH Data Sharing Repositories is related to: RIKEN integrated database of mammals is related to: JAX Neuroscience Mutagenesis Facility is related to: PhenoGO is related to: International Mouse Strain Resource is related to: Mouse Genome Database is related to: Mouse Tumor Biology Database has parent organization: Jackson Laboratory is parent organization of: Anatomy of the Laboratory Mouse is parent organization of: Mouse Genome Informatics Transgenes is parent organization of: Federation of International Mouse Resources is parent organization of: MGI GO Browser is parent organization of: Recombinase (cre) Activity is parent organization of: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource is parent organization of: MGI strains is parent organization of: MPO is parent organization of: Phenotypes and Mutant Alleles is parent organization of: Human Mouse Disease Connection is parent organization of: Functional Annotation is parent organization of: Strains, SNPs and Polymorphisms is parent organization of: Vertebrate Homology is parent organization of: Batch Data and Analysis Tool is parent organization of: Nomenclature |
NHGRI HG000330; NHGRI HG002273; NICHD HD033745; NCI CA089713 |
PMID:19274630 PMID:18428715 |
Free, Freely available | nif-0000-00096, OMICS_01656, r3d100010266 | http://www.informatics.jax.org/batch, http://www.informatics.jax.org/submit.shtml, http://www.informatics.jax.org/expression.shtml, https://doi.org/10.17616/R35P54 | SCR_006460 | , MGI, Mouse Genome Informatics | 2026-08-10 09:32:50 | 1220 | ||||
|
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit Resource Report Resource Website 10+ mentions |
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit (RRID:SCR_006580) | GOEAST | production service resource, data analysis service, analysis service resource, service resource | Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) is a web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. The main function of GOEAST is to identify significantly enriched GO terms among give lists of genes using accurate statistical methods. Compared with available GO analysis tools, GOEAST has the following unique features: * GOEAST supports analysis for data from various resources, such as expression data obtained using Affymetrix, illumina, Agilent or customized microarray platforms. GOEAST also supports non-microarray based experimental data. The web-based feature makes GOEAST very user friendly; users only have to provide a list of genes in correct formats. * GOEAST provides visualizable analysis results, by generating graphs exhibiting enriched GO terms as well as their relationships in the whole GO hierarchy. * Note that GOEAST generates separate graph for each of the three GO categories, namely biological process, molecular function and cellular component. * GOEAST allows comparison of results from multiple experiments (see Multi-GOEAST tool). The displayed color of each GO term node in graphs generated by Multi-GOEAST is the combination of different colors used in individual GOEAST analysis. Platform: Online tool | statistical analysis, gene ontology, high-throughput, microarray, hybridization, gene, 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: Chinese Academy of Sciences; Beijing; China |
National Natural Science Foundation of China 30725014; National Natural Science Foundation of China 90612019; Ministry of Science and Technology of China 2007CB946901; Chinese Academy of Sciences KSCX2-YW-R-134; Chinese Academy of Sciences KSCX2-YW-N-024 |
PMID:18487275 | Free for academic use | biotools:goeast, nlx_149248 | https://bio.tools/goeast | SCR_006580 | Gene Ontology Enrichment Analysis Software Toolkit, Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) | 2026-08-10 09:32:56 | 40 | ||||
|
GeneTerm Linker Resource Report Resource Website 1+ mentions |
GeneTerm Linker (RRID:SCR_006385) | GTLinker | production service resource, data analysis service, analysis service resource, service resource | Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service. | gene, functional annotation, function, functional metagroup, p-value, annotation, web service |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: InterPro has parent organization: Spanish National Research Council; Madrid; Spain |
PMID:21949701 | Acknowledgement requested | OMICS_02227 | SCR_006385 | GeneTerm Linker - post enrichment functional association by non-redundant reciprocal linkage | 2026-08-10 09:32:52 | 2 | ||||||
|
GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | production service resource, data analysis service, analysis service resource, service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-08-10 09:32:47 | 114 | ||||||
|
Magic Resource Report Resource Website 500+ mentions |
Magic (RRID:SCR_006406) | MAGIC | data or information resource, database, service resource | Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. | gene expression, microarray, development stage, annotation, line, perturbation, gene, contrast, pathway, locus tag, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: ArrayExpress is related to: Plant Ontology is related to: Gene Ontology has parent organization: Ghent University; Ghent; Belgium |
PMID:24407224 | biotools:magic, OMICS_02206 | https://bio.tools/magic | SCR_006406 | MAGIC - MAize Gene expressIon Compendium, MAize Gene expressIon Compendium | 2026-08-10 09:32:49 | 709 | ||||||
|
gsGator Resource Report Resource Website |
gsGator (RRID:SCR_012035) | gsGator | production service resource, data analysis service, analysis service resource, service resource | A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks. | linux, windows, gene, orthology, pathway, phenotype, mirna target, molecular network, genomic annotation, function |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:24423189 | Free, Public | OMICS_02233 | SCR_012035 | 2026-08-10 09:34:23 | 0 | |||||||
|
Cerebellar Development Transcriptome Database Resource Report Resource Website 1+ mentions |
Cerebellar Development Transcriptome Database (RRID:SCR_013096) | CDT-DB | data or information resource, atlas, database | Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. | gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development |
is related to: Gene Ontology is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
Brain development, Brain disorder | INCF Japan Node ; Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:18603407 | To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. | nif-0000-00008 | SCR_013096 | 2026-08-10 09:34:49 | 1 | |||||
|
PhenoGO Resource Report Resource Website 1+ mentions |
PhenoGO (RRID:SCR_013646) | data or information resource, database | PhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context - such as the cell type, disease, tissue, and organ - to existing annotations between gene products and Gene Ontology (GO) terms, as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including: the Cell Ontology (CO), phenotypes from the Unified Medical Language System (UMLS), species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy, and specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA). |
uses: WormBase uses: SGD uses: Gene Ontology uses: Mouse Genome Informatics (MGI) uses: FlyBase is related to: WormBase is related to: SGD is related to: Gene Ontology is related to: Mouse Genome Informatics (MGI) is related to: FlyBase has parent organization: University of Arizona; Arizona; USA |
Available to the research community, Acknowledgement requested | nlx_152722 | www.phenogo.org | SCR_013646 | Phenotype Context Database for Gene Ontology Annotations | 2026-08-10 09:34:52 | 2 | ||||||||
|
dcGO Resource Report Resource Website 10+ mentions |
dcGO (RRID:SCR_014392) | data or information resource, database | A database of domain-centric ontologies on functions, phenotypes, diseases and more. As a biomedical ontology resource, dcGO integrates functional, phenotypic, disease, and drug information. As a protein domain resource, it includes annotations to both the individual domains and supra-domains. Domain classifications and ontologies are organized in hierarchies, and dcGO includes the facility to browse the hierarchies: SCOP Hierarchy for browsing domains, GO Hierarchy for browsing GO terms, and BO Hierarchy for browsing other terms (mostly phenotypes). Users can mine and browse through resources. | database, mining, domain centric ontology, phenotype, human disease, drug, biomedical ontology, protein domain, hierarchy |
uses: Gene Ontology has parent organization: University of Bristol; Bristol; United Kingdom |
PMID:23161684 | Acknowledgement required, Both flat files and MySQL tables are available for download | SCR_014392 | 2026-08-10 09:35:02 | 27 | |||||||||
|
Automated Microarray Pipeline Resource Report Resource Website |
Automated Microarray Pipeline (RRID:SCR_001219) | AMP | production service resource, data analysis service, analysis service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis. | microarray, normalization |
is listed by: OMICtools is related to: Gene Ontology has parent organization: TM4 |
NLM R01-LM008795 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02125 | http://www.tm4.org/amp.html | SCR_001219 | TM4 AMP, AMP: Automated Microarray Pipeline, AMP (TM4 Microarray Software Suite), TM4 Microarray Software Suite: Automated Microarray Pipeline, TM4 Microarray Software Suite: AMP | 2026-08-10 09:31:23 | 0 | |||||
|
WegoLoc Resource Report Resource Website 1+ mentions |
WegoLoc (RRID:SCR_001402) | WegoLoc | production service resource, data analysis service, analysis service resource, service resource | Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information. | subcellular localization, protein |
is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01636 | SCR_001402 | weighted gene ontology term based subcellular locallization prediction | 2026-08-10 09:31:25 | 4 | |||||||
|
pSTIING Resource Report Resource Website 1+ mentions |
pSTIING (RRID:SCR_002045) | pSTIING | data or information resource, database | A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis. | protein-protein, protein-lipid, protein-small molecule, ligand-receptor interaction, receptor-cell type, transcriptional regulatory module, signal transduction module, inflammation, cell migration, tumorigenesis, protein-protein interaction, transcriptional regulatory network, signalling pathway, interaction, protein interaction, motif, domain, protein, gene |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University College London; London; United Kingdom |
Inflammation, Tumor, Cancer | PMID:16381926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01916 | SCR_002045 | Protein Signalling Transcriptional Interactions and Inflammation Networks Gateway, Protein Signalling Transcriptional Interactions & Inflammation Networks Gateway | 2026-08-10 09:31:36 | 2 | |||||
|
AnimalTFDB Resource Report Resource Website 100+ mentions |
AnimalTFDB (RRID:SCR_001624) | AnimalTFDB | data or information resource, database | A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, dna-binding domain, transcription co-factor, chromatin remodeling factor, gene structure, functional domain, go annotation, protein interaction, ortholog, paralog, 3d structure, pathway, protein-protein interaction, binding site, target, data set, image collection, 3d spatial image, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Ensembl has parent organization: Huazhong University of Science and Technology; Wuhan; China |
Huazhong University of Science and Technology; Wuhan; China ; Fundamental Research Funds for the Central Universities 2010MS045; National Natural Science Foundation of China 31171271 |
PMID:22080564 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153892, OMICS_01856, biotools:animal_tfdb | https://bio.tools/animal_tfdb | SCR_001624 | Animal Transcription Factor Database | 2026-08-10 09:31:31 | 292 | ||||
|
GOToolBox Functional Investigation of Gene Datasets Resource Report Resource Website 10+ mentions |
GOToolBox Functional Investigation of Gene Datasets (RRID:SCR_003192) | GOToolBox | source code, service resource, software resource | The GOToolBox web server provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. The web version of the GOToolBox is free for non-commercial users only. Users from commercial companies are allowed to use the site during a reasonable testing period. For a regular use of the web version, a license fee should be paid. We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license. Platform: Online tool | gene, annotation, statistical analysis, slimmer-type tool, function, cluster, gene association, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Center for Genomic Regulation; Barcelona; Spain |
Action Bioinformatique inter-EPST ; French Ministere de l'Education de la Recherche et de la Technologie ; Fondation pour la Recherche Medicale |
PMID:15575967 | Free, Freely available | nif-0000-30623 | http://burgundy.cmmt.ubc.ca/GOToolBox/ | SCR_003192 | GOToolBox - Functional Investigation of Gene Datasets, GOToolBox : Functional Investigation of Gene Datasets | 2026-08-10 09:31:56 | 35 | ||||
|
T-profiler Resource Report Resource Website 10+ mentions |
T-profiler (RRID:SCR_003452) | T-profiler | production service resource, data analysis service, analysis service resource, service resource | One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool | expression, gene, binding, cellular, transcriptional, gene expression, microarray, gene ontology, transcription factor, binding motif, chip-chip, chip, motif, t-test, statistical analysis, transcriptome, bio.tools |
is listed by: Biositemaps is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Columbia University; New York; USA has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Netherlands Foundation for Technical Research APB.5504; NHGRI R01HG003008 |
PMID:15980543 | Free for academic use | nif-0000-33354, biotools:t-profiler | https://bio.tools/t-profiler | SCR_003452 | T-profiler: Scoring the Activity of Pre-defined Groups of Genes Using Gene Expression Data | 2026-08-10 09:32:01 | 11 | ||||
|
ChannelPedia Resource Report Resource Website 10+ mentions |
ChannelPedia (RRID:SCR_003807) | Channelpedia | data or information resource, database | An information management framework for comprehensive ion channel information. It is a knowledge base system centered on genetically expressed ion channel models and it encourages researchers of the field to contribute, build and refine the information through an interactive wiki-like interface. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models (September 2014). Channelepdia provides an ideal platform to collectively build ion channel knowledge base by accommodating both structured and unstructured data. The current version of Channelpedia contains the following sections : Introduction, Genes, Ontologies, Interactions, Structure, Expression, Distribution, Function, Kinetics and Models. Newly published literature related to ion channels is automatically queried every week from PubMed and added to respective categories. Currently, Channelpedia contains ~180,000 abstracts related to ion channels from Pubmed. | ion channel, model, cell, gene, transcript, ontology, interaction, hodgkinhuxley model, kinetics |
uses: PubMed uses: Gene Ontology uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: UniProt uses: Ensembl uses: IntAct uses: Rat Genome Database (RGD) has parent organization: Blue Brain Project |
PMID:22232598 | The community can contribute to this resource, Free, Public | nlx_158108 | SCR_003807 | Channel pedia | 2026-08-10 09:32:06 | 12 | ||||||
|
INMEX Resource Report Resource Website 10+ mentions |
INMEX (RRID:SCR_004173) | INMEX | production service resource, data analysis service, analysis service resource, service resource | A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. | gene expression, meta-analysis, metabolomics, pathway, gene, metabolite, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: KEGG is related to: Human Metabolome Database has parent organization: University of British Columbia; British Columbia; Canada |
Killam Trust ; Canadian Institutes of Health Research |
PMID:23766290 | Acknowledgement requested | biotools:inmex, OMICS_01546 | https://bio.tools/inmex | SCR_004173 | INtegrative Meta-analysis of EXpression data, INMEX - INtegrative Meta-analysis of EXpression data | 2026-08-10 09:32:12 | 19 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the PRECISE-TBI Resources search. From here you can search through a compilation of resources used by PRECISE-TBI and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that PRECISE-TBI has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on PRECISE-TBI then you can log in from here to get additional features in PRECISE-TBI such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into PRECISE-TBI you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
