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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Nephromine Resource Report Resource Website 10+ mentions |
Nephromine (RRID:SCR_003813) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPHROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data. | kidney, gene expression, visualization, clinical, expression profile, gene, mouse model, microarray |
is listed by: NIDDK Information Network (dkNET) is related to: Nephroseq has parent organization: University of Michigan; Ann Arbor; USA has parent organization: Life Technologies |
Kidney disease, Healthy, Lupus nephritis, Chronic kidney disease, Diabetic nephropathy | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158114 | SCR_003813 | 2026-08-03 09:32:19 | 20 | ||||||||
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Mouse Connectome Project Resource Report Resource Website 10+ mentions |
Mouse Connectome Project (RRID:SCR_004096) | MCP | data or information resource, atlas, database | Three-dimensional digital connectome atlas of the C57Black/6J mouse brain and catalog of neural tracer injection cases, which will eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome viewer. The Image Gallery provides a glimpse into some of the highlights of their data set. Representative images of multi-fluorescent tracer labeling can be viewed, while more in depth examination of these and all other cases can be performed in the iConnectome viewer. Phase 1 of this project involves generating a physical map of the basic global wiring diagram by applying proven, state of the art experimental circuit tracing methods systematically, uniformly, and comprehensively to the structural organization of all major neuronal pathways in the mouse brain. Connectivity imaging data for the whole mouse brain at cellular resolution will be presented within a standard 3D anatomic frame available through the website and accompanied by a comprehensive searchable online database. A Phase 2 goal for the future will allow users to view, search, and generate driving direction-like roadmaps of neuronal pathways linking any and all structures in the nervous system. This could be looked on as a pilot project for more ambitious projects in species with larger brains, such as human, and for providing a reliable framework for more detailed local circuitry mapping projects in the mouse. | tract tracing assay, adult mouse, connectivity, c57bl/6j, brain, olfactory bulb, piriform cortical area, lateral olfactory tract, connectome, neuronal tract tracing, nissl, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse Biomedical Informatics Research Network is related to: BICCN has parent organization: Laboratory of Neuro Imaging |
NIMH MH094360-01A1; NCRR 3P41RR013642-12S3 |
PMID:22891053 | LONI Software License | nlx_143548 | http://www.nitrc.org/projects/mcp | SCR_004096 | UCLA Mouse Project | 2026-08-03 09:32:36 | 28 | ||||
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International Knockout Mouse Consortium Resource Report Resource Website 50+ mentions |
International Knockout Mouse Consortium (RRID:SCR_005574) | IKMC | data or information resource, database | Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs. | gene, knock out mouse, chromosome, allele, c57bl/6, embryonic stem cell, vector, mutant, es cell, genome, targeting, gene list, FASEB list |
is related to: Texas A and M Institute for Genomic Medicine is related to: European Mouse Mutant Archive is related to: CMMR - Canadian Mouse Mutant Repository is parent organization of: EUCOMMTOOLS is parent organization of: North American Conditional Mouse Mutagenesis Project is parent organization of: European Conditional Mouse Mutagenesis Program is parent organization of: Knockout Mouse Project |
European Union ; NHGRI HG004074 |
PMID:22968824 PMID:21677750 |
nlx_146200 | SCR_005574 | 2026-08-03 09:32:52 | 68 | |||||||
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SwissRegulon Resource Report Resource Website 10+ mentions |
SwissRegulon (RRID:SCR_005333) | SwissRegulon | data or information resource, database | A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format. | genome, binding site, transcription factor, genome-wide annotation, annotation, chip-chip, chip-seq, non-coding region, promoter, motif, transcript, regulatory motif, genome browser, FASEB list |
is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:23180783 PMID:17130146 |
Acknowledgement requested | nif-0000-03524, OMICS_00543 | SCR_005333 | SwissRegulon Database | 2026-08-03 09:32:39 | 44 | ||||||
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Spliceman Resource Report Resource Website 1+ mentions |
Spliceman (RRID:SCR_005354) | Spliceman | data analysis service, service resource, analysis service resource, production service resource | An online tool that takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation includes 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish. | dna sequence, pre-mrna, splicing, pre-mrna splicing, point mutation, mutation, sequence variation, fasta |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
PMID:22328782 | Free, Non-commercial, Commercial use requires license | OMICS_02259 | SCR_005354 | 2026-08-03 09:32:39 | 5 | |||||||
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UniPROBE Resource Report Resource Website 100+ mentions |
UniPROBE (RRID:SCR_005803) | UniPROBE | data or information resource, database | Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. | protein, in vitro, dna binding, protein binding, genetics, dna, nucleotide sequence, sequence variant, k-mer, position weight matrix, graphical sequence logo, motif, motif similarity, binding site, microarray, protein-dna interaction, protein binding microarray probe sequence, probe, FASEB list |
is listed by: re3data.org is listed by: OMICtools |
PMID:21037262 PMID:18842628 |
Acknowledgement requested, Academic research use license | nif-0000-03611, OMICS_00546, r3d100010557 | http://thebrain.bwh.harvard.edu/pbms/webworks_pub/, https://doi.org/10.17616/R35C9J | SCR_005803 | UniPROBE Database, Universal Protein Binding Microarray Resource for Oligonucleotide Binding Evaluation, Universal PBM Resource for Oligonucleotide Binding Evaluation | 2026-08-03 09:32:56 | 149 | |||||
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Peptide Sequence Database Resource Report Resource Website |
Peptide Sequence Database (RRID:SCR_005764) | PepSeqDB | data or information resource, database | The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases. | peptide, sequence | has parent organization: Edwards Lab | nlx_149230 | SCR_005764 | 2026-08-03 09:32:56 | 0 | |||||||||
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DisGeNET Resource Report Resource Website 1000+ mentions |
DisGeNET (RRID:SCR_006178) | DisGeNET | data or information resource, database | Database and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature. | gene, disease, gene-disease association, gene-disease ontology, gene-disease text mining, text mining, genotype-phenotype, rdf, genotype, phenotype, gene-disease, variant-disease, FASEB list |
uses: Comparative Toxicogenomics Database (CTD) uses: Genetic Association Database uses: UniProt uses: Mouse Genome Database uses: Reactome uses: Unified Medical Language System uses: Entrez Gene uses: MEDLINE uses: National Center for Biomedical Ontology uses: National Cancer Institute Thesaurus uses: Human Phenotype Ontology uses: Semanticscience Integrated Ontology uses: Cytoscape uses: Literature-derived human gene-disease network uses: Rat Genome Database (RGD) uses: National Library of Medicine uses: PsyGeNET is used by: HmtPhenome is listed by: 3DVC is affiliated with: Gene-Disease Association Type Ontology has parent organization: Pompeu Fabra University; Barcelona; Spain |
EFPIA ; Instituto de Salud Carlos III-Fondo Europeo de Desarrollo Regional ; Elixir-Excelerate ; Innovative Medicines Initiative Joint Undertaking ; European Union Seventh Framework Programme ; European Union Horizon 2020 |
PMID:27924018 PMID:25877637 PMID:21695124 PMID:20861032 |
Restricted | nlx_151710, r3d100013301 | https://doi.org/10.17616/R31NJMR9 | SCR_006178 | database of gene disease associations | 2026-08-03 09:32:55 | 2210 | ||||
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | data analysis service, service resource, analysis service resource, production 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 | 2026-08-03 09:33:02 | 106 | ||||||
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CircaDB Resource Report Resource Website 10+ mentions |
CircaDB (RRID:SCR_018078) | CircaDB | web service, database, data access protocol, data or information resource, software resource | Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans. | Mammalian circadian gene, gene expression, expression profile, mice, human, gene annotation, data, time course expression data | PMID:23180795 | Free, Freely available | http://github.com/itmat/circadb | SCR_018078 | Circadian gene expression profiles DataBase | 2026-08-03 09:36:58 | 19 | |||||||
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CRISPRdirect Resource Report Resource Website 100+ mentions |
CRISPRdirect (RRID:SCR_018186) | production service resource, web service, analysis service resource, data access protocol, service resource, software resource | Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. | CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Japan Science and Technology Agency ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:25414360 | Free, Freely available | biotools:CRISPRdirect | https://bio.tools/CRISPRdirect | SCR_018186 | 2026-08-03 09:36:53 | 452 | ||||||
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Allen Mouse Reference Atlas Ontology Resource Report Resource Website 1+ mentions |
Allen Mouse Reference Atlas Ontology (RRID:SCR_021000) | controlled vocabulary, data or information resource, ontology | Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree. | structure ontology, brain structure, ontology, hierarchical partonomy, anatomical structures |
is used by: Allen Mouse Brain Common Coordinate Framework is used by: Early Postnatal Developmental Mouse Brain Atlas has parent organization: Allen Institute for Brain Science |
PMID:32386544 | Free, Freely available | SCR_021000 | 2026-08-03 09:37:18 | 5 | |||||||||
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Brain Architecture Project Resource Report Resource Website 10+ mentions |
Brain Architecture Project (RRID:SCR_004283) | topical portal, data or information resource, portal | Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts | central nervous system, connectivity, mapping, model, neuroanatomy, organism, post-mortem, structure, nervous system, structure, human, mouse, brain, zebra finch, addiction gene, addiction |
is used by: BICCN lists: Allen Institute for Brain Science lists: University of California at Los Angeles; California; USA is related to: Mouse Brain Architecture Project is related to: BICCN Anatomy and Morphology Project is related to: Allen Institute for Brain Science has parent organization: Cold Spring Harbor Laboratory is parent organization of: Human Brain Connectivity Database is parent organization of: OBART is parent organization of: Zebrafinch Brain Architecture Project is parent organization of: Mouse Brain Architecture Project |
W. M. Keck Foundation ; NIMH ; NIDA ; Crick-Clay Professorship in Biomathematics at CSHL ; Mathers Foundation ; Simons Foundation |
Free, Public | nlx_143664 | SCR_004283 | BrainArchitecture.org, BrainArchitecture | 2026-08-03 09:32:24 | 14 | |||||||
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dkCOIN Resource Report Resource Website 1+ mentions |
dkCOIN (RRID:SCR_004438) | dkCOIN | resource, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO). | gene, adenovirus construct, antibody, co-immunoprecipitation, embryonic stem cell line, functional genomics, histology, mouse strain, pcr primer, protocol, real time pcr, metadata, diabetes, stem cell, metabolism, tissue development, web service, cloud, embryonic stem cell |
is used by: NIF Data Federation is related to: Beta Cell Biology Consortium is related to: NIDDK Information Network (dkNET) is related to: National Mouse Metabolic Phenotyping Centers is related to: Nuclear Receptor Signaling Atlas is related to: Diabetic Complications Consortium is related to: T1DBase is related to: OBO has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIDDK 3U01DK072473-05S3; NIDDK 5U24DK076169; NIDDK U19DK062434 |
PMID:22734043 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44256 | SCR_004438 | NIDDKConsortium Interconnectivity Network | 2026-08-03 09:32:33 | 1 | |||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | data repository, production service resource, service resource, database, source code, storage service resource, analysis service resource, data or information resource, software resource, data set | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-08-03 09:32:40 | 2 | ||||
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Mouse Brain Architecture Project Resource Report Resource Website 1+ mentions |
Mouse Brain Architecture Project (RRID:SCR_004683) | d spatial image, reference atlas, data or information resource, atlas | An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset. | atlas, brain, brain architecture, connectivity, mouse brain architecture, neuroanatomy |
is related to: Brain Architecture Project has parent organization: Brain Architecture Project |
NIH Office of the Director ; NIMH RC1MH088659; NIMH R01MH087988 |
Fully accessible to the neuroscience community as well as interested members of the general public, Acknowledgement requested | nlx_146201 | http://www.brainarchitecture.org | http://www.brainarchitecture.org/mouse/about | SCR_004683 | MBA Project, Mouse Brain Architecture | 2026-08-03 09:32:40 | 5 | |||||
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VARIANT Resource Report Resource Website 1000+ mentions |
VARIANT (RRID:SCR_005194) | VARIANT | production service resource, data analysis service, software application, data processing software, data analysis software, analysis service resource, service resource, software resource | Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional property, variant, gene, non-coding region, mirna, function, single nucleotide variant, next generation sequencing, command line |
is listed by: OMICtools has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Science and Innovation BIO2011-27069 | PMID:22693211 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00193 | SCR_005194 | Variant effect, VARIant ANalysis Tool | 2026-08-03 09:32:50 | 1366 | |||||
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SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | production service resource, data analysis service, analysis service resource, service resource, software resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SeqAnt - Sequence Annotator | 2026-08-03 09:32:37 | 2 | ||||||
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PRISM (Stanford database) Resource Report Resource Website 10000+ mentions |
PRISM (Stanford database) (RRID:SCR_005375) | PRISM | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, transcription factor, function, transcription factor binding site, transcription factor regulator, biological role, target gene, target genomic region, genome, FASEB list |
is listed by: OMICtools is listed by: SoftCite is related to: GREAT: Genomic Regions Enrichment of Annotations Tool has parent organization: Stanford University School of Medicine; California; USA |
PMID:23382538 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00489 | SCR_005375 | Predicting Regulatory Information from Single Motifs | 2026-08-03 09:32:52 | 40813 | ||||||
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TRANSPATH Resource Report Resource Website 1+ mentions |
TRANSPATH (RRID:SCR_005640) | TRANSPATH | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. | signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression |
is related to: TRANSFAC is related to: GeneTrail has parent organization: BIOBASE Corporation |
BMBF 031U210B; BMBF 0313092; European Union FP6 contract LSHG-CT-2004-503568; European Union MRTN-CT-2004-512285 |
PMID:18629064 PMID:16381929 PMID:12519957 PMID:11724734 |
Free for academic use, Free for non-profit use, Account required | nif-0000-03580 | http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html | SCR_005640 | 2026-08-03 09:32:44 | 2 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
