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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood Resource Report Resource Website 1+ mentions |
3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood (RRID:SCR_009437) | 3D DTI Atlas of the Rat Brain | atlas, data or information resource, reference atlas | 3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file. | magnetic resonance, adult rat, newborn rat, infant rat, young rat, sprague dawley, male, female |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Control, Normal | UNC Neurodevelopment Disorders Research Center ; NICHD HD 03110; NINDS R41 NS059095; NIDA IP01DA022446-02 |
nlx_155577 | SCR_009437 | 3-Dimensional Diffusion Tensor Imaging (DTI) Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood | 2026-09-12 01:00:59 | 2 | ||||||
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Disease Genes Conserved Sequence Tags Database Resource Report Resource Website |
Disease Genes Conserved Sequence Tags Database (RRID:SCR_000760) | data or information resource, database | A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions. | database, conserved sequence element, genomic sequence, human gene, pathogenesis, genetic disorder, blastz, cst | Telethon Foundation ; the Associazione Italiana per la Ricerca sul Cancro (AIRC) ; the Federazione Italiana per la Ricerca sul Cancro (FIRC) ; the Italian Ministry for Research (MURST) ; the National Council for Research (CNR) ; Regione Campania ; BioGeM |
PMID:15608249 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21121 | SCR_000760 | DG CST Database | 2026-09-12 01:01:20 | 0 | |||||||
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MitoMiner Resource Report Resource Website 50+ mentions |
MitoMiner (RRID:SCR_001368) | data or information resource, database | A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java. | mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, ortholog, FASEB list |
uses: HomoloGene uses: UniProt uses: KEGG uses: OMIM uses: The Human Protein Atlas uses: Gene Ontology |
MRC | PMID:22121219 PMID:19208617 |
Public, Acknowledgement requested, Code: | nlx_152504 | SCR_001368 | MitoMiner - A database of the mitochondrial proteome | 2026-09-12 01:01:22 | 78 | ||||||
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BodyMap-Xs Resource Report Resource Website 1+ mentions |
BodyMap-Xs (RRID:SCR_001147) | BodyMap-Xs | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008 | expressed sequence tag, comparative genomics, anatomy, taxonomy, brain, blood, connective, reproductive, muscular, alimentary, lung, liver, urinary, endocrine, exocrine, embryo, homology, gene expression, ortholog, paralog | has parent organization: DNA DataBank of Japan (DDBJ) | Neoplasm, Normal | Japanese Ministry of Education Culture Sports Science and Technology MEXT ; New Energy and Industrial Technology Development Organization |
PMID:16381946 PMID:11125076 PMID:10592203 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02617 | http://bodymap.jp/, http://bodymap.ims.u-tokyo.ac.jp/ | SCR_001147 | BodyMap-Xs: anatomical and taxonomical breakdown of animal EST, BodyMap, BodyMap- human and mouse gene expression database, BodyMap: human and mouse gene expression database, BodyMap-cross species, BodyMap-Xs(cross species) | 2026-09-12 01:01:21 | 1 | |||
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CORUM Resource Report Resource Website 100+ mentions |
CORUM (RRID:SCR_002254) | CORUM | data or information resource, database |
Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded. The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
mammalian protein, protein, protein complex, protein function, FASEB list |
is listed by: OMICtools is related to: Interaction Reference Index is related to: ConsensusPathDB has parent organization: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany |
BMBF 031U212C | PMID:19884131 PMID:17965090 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02688, OMICS_01904, r3d100011272 | http://mips.gsf.de/genre/proj/corum | SCR_002254 | CORUM the Comprehensive Resource of Mammalian protein complexes, CORUM - the Comprehensive Resource of Mammalian protein complexes | 2026-09-12 01:01:25 | 164 | ||||
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Surface-Based Atlases Resource Report Resource Website 1+ mentions |
Surface-Based Atlases (RRID:SCR_002099) | Caret:Atlases | atlas, data or information resource, database | THIS RESOURCE IS NO LONGER IS SERVICE. Documented on July,29,2022. Surface-based atlases of human, macaque, rat and mouse cerebral and cerebellar cortices derived from structural MRI volumes developed in the Van Essen laboratory can be downloaded by direct links on the SumsDB database and can be viewed using freely available Caret (offline) and WebCaret (online) software. The human and macaque atlases include a large and growing compendium of experimental data pertaining to the structural and functional organization of primate cerebral cortex. | atlas, human, macaque, mouse, cerebral cortex, cerebellar cortex, database, primate, magnetic resonance imaging, neuroanatomy |
is listed by: Biositemaps has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22052704 | THIS RESOURCE IS NO LONGER IS SERVICE. | nif-0000-00346 | SCR_002099 | Surface-Based Atlas | 2026-09-12 01:01:24 | 2 | ||||||
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cisRED: cis-regulatory element Resource Report Resource Website 10+ mentions |
cisRED: cis-regulatory element (RRID:SCR_002098) | cisRED | data or information resource, database | Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species. | atomic motif, conserved sequence motif, motif pattern, regulatory element, motif, atomic, promoter, chip-seq, transcription factor binding site, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: BC Cancer Agency |
Genome Canada ; BC Cancer Foundation ; Michael Smith Foundation for Health Research |
PMID:16381958 | Free, Freely available | nif-0000-02665, biotools:cisred, OMICS_01857, r3d100010619 | https://bio.tools/cisred, https://doi.org/10.17616/R3XK69 | SCR_002098 | cisRED - Databases of genome-wide regulatory module and element predictions | 2026-09-12 01:01:24 | 14 | ||||
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RESNET Resource Report Resource Website 1000+ mentions |
RESNET (RRID:SCR_002121) | ResNet | data or information resource, database | Databases that represent sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using Ariadne's MedScan technology. ResNet databases store information harvested from the entire PubMed in a formal structure that allows searching, retrieval and updating by Pathway Studio user. ResNet is seamlessly installed when Pathway Studio is installed. There are several available ResNet databases: *ResNet Mammalian Database includes data for Human, Rat, and Mouse *ResNet Plant Database has data on Arabidopsis, Rice and several other plants. Features of ResNet: *All extracted relations have linked access to the original article or abstract *Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results *Users can update ResNet as often as required using the MedScan technology built into all Ariadne products *Updates are made available by Ariadne every quarter To purchase Pathway Studio software with ResNet database, for information, or to schedule a web demonstration, call our sales department at (240) 453-6272, or (866) 340-5040 (toll free)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | biological relationship, biomedical, literature, interaction, FASEB list |
is listed by: Biositemaps has parent organization: Indiana University School of Medicine; Indiana; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20909 | http://www.ariadnegenomics.com/products/databases/ariadne-resnet/ | SCR_002121 | Ariadne ResNet Databases, ResNet Databases | 2026-09-12 01:01:24 | 1384 | ||||||
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Transgenic Animal Model Core Resource Report Resource Website 1+ mentions |
Transgenic Animal Model Core (RRID:SCR_000776) | TAMC | biomaterial supply resource, material resource | A service for preparing genetically modified mice and rats for investigators at the University of Michigan. These mice models are typically used to study gene function, gene expression, gene regulation, and for the development of animal models of human disease and gene therapy reagents. TAMC provide access to their micromanipoulation and embryos stem cell workstations along with necessary reagents such as specialized plasmids, embryonic stem (ES) cell lines, FBS, and feeder cells certified for ES cell culture. | trangenic, mouse, modify, reagent, cell, toxigene, micromanipulation, embryo, stem, plasmid, culture, transgene, mouse, disease | has parent organization: University of Michigan; Ann Arbor; USA | NIH Intramural Research Program | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30059 | SCR_000776 | Transgenic Animal Model Core (TAMC) | 2026-09-12 01:02:24 | 4 | ||||||
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Resource Identification Portal Resource Report Resource Website 10+ mentions |
Resource Identification Portal (RRID:SCR_004098) | RII Portal | data or information resource, portal | Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource. | antibody, organism, service resource, software resource, database, resource, identifier, citation, biomedical, publication, research resource identifier, rrid, ASWG |
uses: Antibody Registry uses: SciCrunch Registry uses: Mouse Genome Informatics (MGI) uses: Zebrafish Information Network (ZFIN) uses: Rat Genome Database (RGD) uses: WormBase uses: FlyBase recommends: SciCrunch Registry recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: Rat Genome Database (RGD) is recommended by: Neuroscience Information Framework is recommended by: SciCrunch Registry is related to: NIF Data Federation has parent organization: SciCrunch |
NIGMS R24 GM144308 | The community can contribute to this resource | nlx_158572 | SCR_004098 | Resource Identification Initiative Portal | 2026-09-12 01:02:32 | 20 | ||||||
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Waxholm Space Atlas of the Sprague Dawley Rat Brain Resource Report Resource Website 10+ mentions |
Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) | WHS-SD-atlas | atlas, data or information resource, waxholm atlas | Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format. | volumetric, atlas, anatomical, delineation, rat, brain, structural, contrast, isotropic, MIR, DTI, male, Sprague Dawley, image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP is related to: PMOD Software is related to: Duke University; North Carolina; USA has parent organization: University of Oslo; Oslo; Norway works with: MeshView works with: VisuAlign |
EC Human Brain Project ; NCI U24 CA092656; NIBIB P41 EB015897; Research Council of Norway |
PMID:24726336 PMID:25585022 |
Free, Available for download, Freely available | SCR_017124 | WHS SD rat atlas, WHS_SD_rat_atlas, WHS-SD-rat-atlas | 2026-09-12 01:02:17 | 38 | ||||||
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LocaliZoom Resource Report Resource Website 1+ mentions |
LocaliZoom (RRID:SCR_023481) | software resource, web application | Web application for displaying high-resolution image series coupled with overlaid atlas delineations. Online pan-and-zoom type viewer with three operating modes: Display series with atlas overlay, both linear and nonlinear alignments are supported; Create or edit nonlinear alignments; Create markup which can be exported as MeshView point clouds or to Excel for further numerical analysis. | Nonlinear refinement, 2D, 3D, registration, quantitative analysis, residual anatomical variability |
is related to: QuickNII is related to: VisuAlign is related to: MeshView is related to: SeriesZoom has parent organization: University of Oslo; Oslo; Norway |
EU Horizon 2020 Framework Partnership Agreement No. 650003 (HBP FPA) | Fully available for own deployment (open source, MIT license), or available as a service (free of charge, but registration is required) via EBRAINS ( https://ebrains.eu/register/ ) | https://localiview.apps.ebrains.eu/, https://tevemadar.github.io/LocaliZoom/, https://github.com/Tevemadar/LocaliZoom | SCR_023481 | 2026-09-12 01:00:39 | 4 | ||||||||
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M-Track Resource Report Resource Website 1+ mentions |
M-Track (RRID:SCR_015865) | data processing software, software application, software resource, source code | Source code that allows users to simultaneously track the movement of individual paws during spontaneous grooming episodes and walking in multiple freely-behaving mice/rats. This toolbox provides a simple platform to perform trajectory analysis of paw movement. | mouse, rat, grooming, paw tracking, movement tracking, free behavior experiment, trajectory analysis | PMID:27636358 | Open source, Available for download, Runs on Windows, Runs on Linux | SCR_015865 | 2026-09-12 12:58:31 | 2 | ||||||||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
Baylor College of Medicine Medical Scientist Training Program ; Belfer Foundation ; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; NCI P30 CA06516; NCRR R24 RR032668; NHGRI U01 HG007709; NIGMS R01 GM067761; NIGMS R01 GM067858; NIGMS R01 GM084947; NIGMS R01 GM120033; NIH Office of the Director R24 OD021997; NIH Office of the Director R24 OD022005; NINDS 1U54NS093793; NINDS U54 NS093793; NSF DMS 1263932; Simons Foundation ; T T Chao Family Foundation ; The Robert and Janice McNair Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-09-12 12:58:45 | 25 | ||||
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miRquant Resource Report Resource Website 1+ mentions |
miRquant (RRID:SCR_017261) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications. | annotation, quantification, miRNA, smRNA-seq, data, functionally, distinct, isoform, isomiR, quality, sequencing, genome, mapping, statistic, tDR, yDR | PMID:28187421 | Free, Available for download, Freely available | SCR_017261 | miRquant 2.0 | 2026-09-12 12:58:50 | 1 | |||||||||
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IITC Incapacitance Meter Resource Report Resource Website |
IITC Incapacitance Meter (RRID:SCR_016143) | resource | Hardware that is used to test and assess pain and inflammation of the hind limbs on mice and rats. Dynamic weight bearing enables the test to be implemented on both limbs, while inflicting less stress on the subject animal. | hardware, equipment, instrument, pain, inflammation, mice, rat, limb | PMID:28326938 | Commercially available | SCR_016143 | The IITC Incapacitance Test Meter, Incapacitance Meter | 2026-09-12 12:58:35 | 0 | |||||||||
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GermOnline Resource Report Resource Website 10+ mentions |
GermOnline (RRID:SCR_002807) | GermOnline | data or information resource, database | Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | fertility, development, germline, microarray, annotation, in vivo, protein-dna binding, protein-protein interaction, genome, ortholog, high-density oligonucleotide microarray, gene expression, genome annotation, gene orthology, genechip, tiling array, development, meiosis, gametogenesis, mitotic cell cycle, data set, data repository, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: OMA Browser has parent organization: National Institute of Health and Medical Research; Rennes; France |
Swiss Institute of Bioinformatics ; bioinformatics platform of Biogenouest ; National Institute of Health and Medical Research; Rennes; France ; University of Rennes 1; Rennes; France |
PMID:21149299 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:germonline, nif-0000-02906, r3d100010248 | https://bio.tools/germonline, https://doi.org/10.17616/R37K5Q | SCR_002807 | 2026-09-12 01:01:26 | 17 | |||||
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HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | data or information resource, database, service resource | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | NCBI HomoloGene | 2026-09-12 01:01:27 | 459 | |||||
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Knowledgebase for Addiction Related Genes Resource Report Resource Website 1+ mentions |
Knowledgebase for Addiction Related Genes (RRID:SCR_002687) | KARG | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database of data and knowledge linking genes and chromosome regions to addiction that were extracted from reviewing more than 1,000 peer-reviewed publications from between 1976 and 2006. This list of publications included review papers on addiction selected from results of PUBMED query "(addiction OR drug abuse) AND review" as well as research papers selected from PUBMED query "(addiction OR drug abuse) AND (gene OR microarray OR proteomics OR QTL OR population association OR genetic linkage)". The data spanned multiple technology platforms including classical hypothesis-testing of single genes, identification of significantly differentially expressed genes in microarray experiments, identification of significantly differentially expressed proteins in proteomics assays, identification of addiction-vulnerable chromosome regions in animal QTL studies, genetic linkage studies, population association studies, and OMIM annotations. From each publication they collected the genes, proteins, or chromosome regions linked to addiction, as well as metadata such as species, nature of the addictive substance, studied brain regions, technology platforms, and experimental parameters. In total, they collected 2,343 items of evidence linking 1,500 human genes to addiction. Among them 396 genes were supported by two or more items of evidence. The interface supports browsing of the genes by chromosome or pathways, advanced text search by gene ID, organism, type of addictive substance, technology platform, protein domain, and/or PUBMED ID, and sequence search by BLAST similarity. All data, database schema, and MySQL commands are freely available for download. | molecular neuroanatomy resource, gwas, meta-analysis, genetic susceptibility, gene, protein, chromosome, pathway, drug of abuse, blast, addiction, substance abuse, drug abuse, microarray, proteomics, qtl, population association, genetic linkage |
uses: PubMed has parent organization: Peking University; Beijing; China |
PMID:18179280 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00411 | SCR_002687 | KARG: Knowledgebase for Addiction-Related Gene, Knowledgebase for Addiction-Related Gene, KARG: Knowledgebase for Addiction Related Genes | 2026-09-12 01:01:26 | 8 | ||||||
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ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters Resource Report Resource Website 1+ mentions |
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters (RRID:SCR_002276) | ABS | data or information resource, database | Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available. | gene, alignment, annotation, binding, computational, genome, nucleotide, ortholog, prediction, promoter, sequence, target, transcription, transcriptional factor, binding site, promoter sequence, protein motif, benchmark, transcription factor binding site, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IntegromeDB has parent organization: Center for Genomic Regulation; Barcelona; Spain |
European Union FP6 contract LSHG-CT-2003-503265 | PMID:16381947 | Acknowledgement requested, GNU General Public License, v2 | biotools:alggen, nif-0000-21006 | https://bio.tools/alggen | SCR_002276 | A database of Annotated regulatory Binding Sites from orthologous promoters | 2026-09-12 01:01:25 | 3 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
