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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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RPCI Gene Targeting and Transgenic Shared Resource Resource Report Resource Website |
RPCI Gene Targeting and Transgenic Shared Resource (RRID:SCR_001020) | access service resource, core facility, service resource | Facility which provides researchers with transgenic mouse technologies, methods, and animal models. Knockout mice, transgenic mice, and mice on multiple strain backgrounds are provided. | core facility, mouse, animal model, transgenic, knockout, cancer, shared resource |
is listed by: ScienceExchange has parent organization: Roswell Park Comprehensive Cancer Center |
NCI P30CA16056 | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_10094 | http://www.scienceexchange.com/facilities/gene-targeting-and-transgenic-facility | SCR_001020 | RPCI Gene Targeting and Transgenic Facility, Roswell Park Cancer Institute Gene Targeting and Transgenic Facility, Roswell Park Cancer Institute Gene Targeting and Transgenic Shared Resource | 2026-09-19 12:58:31 | 0 | ||||||
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CAGE Basic Viewer for Mus musculus Resource Report Resource Website 1+ mentions |
CAGE Basic Viewer for Mus musculus (RRID:SCR_000451) | CAGE Basic Viewer | data or information resource, data set | A web system, which could search and display to current CAGE library information in CAGE Database. | genome, gene, tissue, library, map, clone, cage, tag, mus musculus, primer, cdna, transcription, mouse development, theiler stage |
is related to: Functional Annotation of the Mammalian Genome is related to: CAGE has parent organization: RIKEN |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30231 | SCR_000451 | 2026-09-19 12:58:30 | 1 | ||||||||
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Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project Resource Report Resource Website 1+ mentions |
Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project (RRID:SCR_000726) | Mouse Resequencing Project | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Data, grouped by chromosome, available as flat files for download, of identified DNA polymorphisms (SNPs) in 15 commonly used strains of inbred laboratory mice. Perlegen's SNP, genotype (empirical and imputed), haplotype, trace, and PCR primer data has been compiled with NCBI Mouse Build information to produce data files for public use. Using high-density oligonuclueotide array technology, the study identified over 8 million SNPs and other genetic differences between these strains and the previously sequenced C57BL/6J reference strains (Phase 1). By leveraging data provided by Mark Daly's research team at the Broad Institute, genotypes were also predicted for 40 other common strains (Phase 2). Under an extension to the contract, Eleazar Eskin's group at UCLA has used this data to evaluate SNP associations with phenotypes from the Mouse Phenome Project (the Mouse Phenome Database), and to construct haplotype maps for a total of 94 inbred strains (the Mouse HapMap Project). SNP and genotype positions have been mapped from their original reference coordinates to NCBI Mouse Build 37 coordinates. Note that C57BL6/J strain was not selected for re-sequencing as this data would have been almost entirely redundant with the NCBI reference sequence. Since we did not actually determine genotypes for C57BL6/J, we did not submit genotypes for this strain to dbSNP. However, implicit genotypes for C57BL6/J can be obtained from the reference sequence at each SNP position (the reference allele is the first allele in the ALLELES column). The data is available for download in two different compressed file formats. The files are saved as both PC .zip files and Unix compressed .gz files. At this website, you can: * Learn more about the goals of the Perlegen mouse resequencing project. * Learn more about the array-based resequencing technology used in the project. * Download the SNPs, genotypes, and other data generated by the project, plus sequences of the long-range PCR primers used for SNP discovery. * Browse the mouse genome for SNPs. * View the haplotype blocks within the mouse genome. Mouse Genome Browser The Mouse Genome Browser can be used to visualize genes and the SNPs discovered in this study of genome-wide DNA variation in 15 commonly used, genetically diverse strains of inbred laboratory mice. The reference genome is the C57BL/6J strain NCBI build 37 mouse sequence. In addition to the experimentally-derived genotypes for the original 15 strains, the imputed genotypes for 40 additional inbred mouse strains can also be accessed. Mouse Haplotype Analysis The sequences of 16 commonly used, genetically diverse strains of inbred laboratory mice were analyzed to determine their haplotype structure. The Ancestry Browser shows which ancestral sequence each inbred strain most resembles, along with statistics on the pairwise similarity between the ancestral strains. The Haplotype Viewer shows the haplotype block boundaries and the pairwise similarity for all 56 strains: the 15 used for SNP discovery, the reference strain (C57BL/6J), and the 40 additional strains for which the genotypes were imputed. | genetic variation, chromosome, dna, genome, genotype, haplotype, oligonuclueotide, inbred mouse strain, polymorphism, sequence, single-nucleotide polymorphism, c57bl6/j | is related to: Mouse HapMap Imputation Genotype Resource | NIEHS ; HHSN29120045530C (N01-ES-45530) |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21746 | SCR_000726 | 2026-09-19 12:58:31 | 3 | |||||||
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ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-09-19 12:58:33 | 35 | ||||||
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Mouse HapMap Imputation Genotype Resource Resource Report Resource Website 1+ mentions |
Mouse HapMap Imputation Genotype Resource (RRID:SCR_002576) | Mouse HapMap | data or information resource, data set | Genetic maps for 94 inbred strains of mouse and imputed genotypes using the NIEHS / Perlegen resequencing resource. Combining with the 13,094 Wellcome Trust SNPs (Single-nucleotide polymorphisms), a set of 132,285 SNPs was compiled and is available for download. Using the mouse HapMap resource, it is possible to accurately impute the genotypes of the 94 strains at the 8 million SNPs discovered by the NIEHS/Perlegen mouse resequencing project. They imputed the genotypes at the NIEHS/Perlegen SNPs from the mouse HapMap SNPs and an additional set of 7,570 gap-filling SNPs provided by NIEHS/Perlegen. Since each NIEHS/Perlegen SNP probe has different quality, they classified roughly half of the SNPs as "high-quality" SNPs, which do not have missing genotype at any of the 15 resequenced strains. The imputed genotypes are available for the high-quality SNPs, which has estimated error rate of 0.27% for high-confidence imputed genotypes. In addition, the imputed genotypes for all 8 million SNPs are also available for download. Their estimated error rate is 0.37% for high-confidence imputed genotypes. | genetic variation, genotype, haplotype, imputed genotype, inbred mouse strain, imputed, phenotype, single-nucleotide polymorphism |
is related to: Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project has parent organization: University of California at Los Angeles; California; USA |
NIEHS | nif-0000-21752 | SCR_002576 | 2026-09-19 12:58:34 | 5 | ||||||||
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Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | 2026-09-19 12:58:35 | 3 | |||||||
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CistromeFinder Resource Report Resource Website 1+ mentions |
CistromeFinder (RRID:SCR_005405) | CistromeFinder | data or information resource, data set | Data portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations (May 2013). Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update. | chip-seq, dnase-seq, cell, tissue, disease, histone modification, transcription factor, chromatin regulator, dnase, binding site, gene, transcription regulation |
is listed by: OMICtools is related to: UCSC Genome Browser is related to: CistromeMap has parent organization: Dana-Farber Cancer Institute |
PMID:23508969 | The community can contribute to this resource | OMICS_00528 | SCR_005405 | 2026-09-19 12:58:37 | 2 | |||||||
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Target genes of Wnt/beta-catenin signaling Resource Report Resource Website 10+ mentions |
Target genes of Wnt/beta-catenin signaling (RRID:SCR_007022) | Target genes of Wnt/beta-catenin signaling | data or information resource, data set | A list of target genes of Wnt/beta-catenin signaling. Suggestions for additions are welcome. Direct targets are defined as those with Tcf binding sites and demonstrating that these sites are important. | target gene, wnt/beta-catenin signaling, wnt, beta-catenin, signaling, gene | has parent organization: Stanford University; Stanford; California | Colon cancer, Tumor, Adenocarcinoma, Melanoma, Cancer | The community can contribute to this resource | nlx_156867 | SCR_007022 | 2026-09-19 12:58:39 | 24 | |||||||
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UniProt Chordata protein annotation program Resource Report Resource Website |
UniProt Chordata protein annotation program (RRID:SCR_007071) | Chordata protein annotation program | data or information resource, data set | Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms. | chordata, protein, protein annotation, functional annotation, human, non-human vertebrate, xenopus laevis, xenopus tropicalis, zebrafish, protein sequence, protein sequencing, nucleotide sequence, sequence, annotation, sequence variant, disease, proteome, gold standard |
is related to: Human Proteomics Initiative is related to: UniProtKB has parent organization: UniProt |
nlx_143879 | SCR_007071 | 2026-09-19 12:58:39 | 0 | |||||||||
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Integrated Nervous System Connectivity Resource Report Resource Website |
Integrated Nervous System Connectivity (RRID:SCR_006391) | NSC | data or information resource, data set | A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references. | connectivity, nervous system, macaque, brain, bird, data set |
uses: Avian Brain Circuitry Database uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat uses: Connectome Wiki uses: BrainMaps.org uses: CoCoMac uses: Brain Architecture Management System uses: BlueBrain Bluima Connectivity is used by: NIF Data Federation has parent organization: Integrated |
Data are licensed by their respective owners, Use and distribution is subject to the terms of use by the original resource | nif-0000-07732 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-8 https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-8, http://neuinfo.org/nif/nifgwt.html?query=nif-0000-07732, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nif-0000-07732-1 | SCR_006391 | NIF Integrated Nervous System Connectivity View, Neuroscience Information Framework Integrated Nervous System Connectivity, Integrated NSC View, Integrated NSC, NIF NSC, NIF Integrated NSC, Integrated Nervous System Connectivity View, Nervous System Connectivity | 2026-09-19 12:58:38 | 0 | ||||||
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4D Nucleome Resource Report Resource Website 10+ mentions |
4D Nucleome (RRID:SCR_016925) | data or information resource, portal, project portal | Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes. | nuclear, organization, gene, expression, cellular, function, normal, development, disease, map, structure, human, mouse, genome |
is listed by: NIDDK Information Network (dkNET) is related to: International Human Epigenome Consortium |
NIH Common Fund | PMID:28905911 | Public | SCR_016925 | 4D Nucleome Network; 4DN Web Portal, The 4D nucleome project, 4DN Portal | 2026-09-19 12:56:06 | 30 | |||||||
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Allen Mouse Brain Common Coordinate Framework Resource Report Resource Website 100+ mentions |
Allen Mouse Brain Common Coordinate Framework (RRID:SCR_020999) | Allen CCF, CCFv3 | atlas, data or information resource, reference atlas | 3D reference atlas to use with online datasets or as standalone resources. Can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D. Intensity and shape population average template brain serves as basis of reference space and coordinate system. Average was constructed at 10 um voxel resolution by interpolating high resolution serial two photon tomography images from young adult C57BL/6J mice. Using multimodal reference data, entire brain was directly parcellated in 3D, labeling every voxel with brain structure from Allen Mouse Reference Atlas Ontology. In the 2017 release, the parcellation spanned 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures. | 3D anatomical reference atlas, brain anatomy, adult mouse brain images |
uses: Allen Mouse Reference Atlas Ontology uses: ccf_streamlines is used by: BICCN is used by: Early Postnatal Developmental Mouse Brain Atlas is related to: Allen Mouse Brain Reference Atlas is related to: Allen Mouse Brain Connectivity Atlas is related to: Allen Brain Atlas API is related to: Developmental Mouse Brain atlas is related to: 3D Developmental Mouse Brain Common Coordinate Framework has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science |
PMID:32386544 | Free, Freely available | https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359 | SCR_020999 | The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas | 2026-09-19 12:56:11 | 319 | ||||||
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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 | 2026-09-19 12:55:35 | 4 | ||||||||
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NEIBank Resource Report Resource Website 10+ mentions |
NEIBank (RRID:SCR_007294) | NEIBank | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | An integrated resource for genomics and bioinformatics in vision research including expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAST search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. To see the same region at the full UCSC site, cut and paste the location from the position window of the genome browser. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. | ear, taste, genetics, cdna, chicken, ciliary body, cornea, fovea, dog, guinea pig, human, iris, lacrimal gland, lens, mouse, ocular surface system, optic nerve, rabbit, rat, retina, rpe, choroid, sequence data, trabecular meshwork, whole eye, zebrafish, library, vision, eye, gene, library, disease, loci, ocular genomics, cdna library, expressed sequence tag, blast, cataract, cornea, glaucoma, myopia, retinal disease, genomics, eye tracking device | has parent organization: National Eye Institute (NEI) Commons | Eye disease, Cataract, Glaucoma, Myopia, Retinal disease | NIH Blueprint for Neuroscience Research ; NEI R01 EY13315; NEI R01 EY11286; NEI P30EY0054722 |
PMID:18648525 | nif-0000-00097 | SCR_007294 | NEI Bank | 2026-09-19 12:55:10 | 15 | |||||
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FreezeScan Resource Report Resource Website 100+ mentions |
FreezeScan (RRID:SCR_014495) | data acquisition software, data processing software, software application, software resource | Software for detecting the onset and completion of freezing behavior of a rodent. It outputs the freezing behaviors as a sequential list, allowing for further statistical analysis. Freezescan detects freezing behaviors, random intervals, interval freezing, and activity levels. It also detects animal activity during the experiment and can output in quantitative and graphical form. | behavior recognition, animal behavior analysis, animal behavior, freezing, freezing behavior, data acquisition software | http://cleversysinc.com/CleverSysInc/wp-content/uploads/2013/02/Datasheet-FreezeScan.pdf | SCR_014495 | 2026-09-19 12:55:14 | 128 | |||||||||||
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Boston Children's Hospital Center of Excellence in Molecular Hematology Resource Report Resource Website |
Boston Children's Hospital Center of Excellence in Molecular Hematology (RRID:SCR_015348) | access service resource, data or information resource, disease-related portal, portal, resource, service resource, topical portal | Research center investigating molecular hematology through mouse and zebrafish models. | hematology research, hematology research center, online portal |
is listed by: NIDDK Information Network (dkNET) is parent organization of: Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core is parent organization of: Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core is parent organization of: Boston Children's Hospital Center of Excellence in Molecular Hematology Mouse Embryonic Stem(ES) Cell and Gene Targeting Core has organization facet: Boston Children's Hospital Center of Excellence in Molecular Hematology Mouse Embryonic Stem(ES) Cell and Gene Targeting Core has organization facet: Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core has organization facet: Boston Children's Hospital Center of Excellence in Molecular Hematology Stem Cell Engineering and Analysis Core is organization facet of: Hematology Centers |
NIDDK U54DK110805 | Available to the research community | SCR_015348 | 2026-09-19 12:55:14 | 0 | |||||||||
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GeneRecommender Resource Report Resource Website 1+ mentions |
GeneRecommender (RRID:SCR_022670) | GenRec | data access protocol, software resource, web service | Platform for helping science researchers by recommending gene symbol obtained by AI neural proprietary network able to scan millions of papers. Web tool to extract hidden patterns and correlations among genes and diseases from scientific papers. | TheProphetAI s.r.l, gene recommender, protein recommender, pathway discover, neural network | Restricted | SCR_022670 | 2026-09-19 12:55:24 | 1 | ||||||||||
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Mouse Experimental Design Ontology Resource Report Resource Website |
Mouse Experimental Design Ontology (RRID:SCR_003879) | MEDO | controlled vocabulary, data or information resource, ontology | Ontology of experimental design for high-throughput mouse analysis pipelines. | owl | is listed by: BioPortal | nlx_157487 | SCR_003879 | 2026-09-19 12:55:06 | 0 | |||||||||
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MOPED - Model Organism Protein Expression Database Resource Report Resource Website 1+ mentions |
MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) | MOPED | analysis service resource, data analysis service, data or information resource, database, production service resource, resource, service resource | An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. | protein expression, gene expression, model organism, gene, protein, pathway, proteomics, transcriptomics, data visualization, overlap plot, heatmap, dot plot, data sharing, protein localization, gene localization |
is related to: GeneCards is related to: UniProt is related to: KEGG is related to: Reactome |
Robert B McMillen Foundation ; NSF DBI0544757; NIGMS 5R01GM076680; NIDDK UO1DK072473; NIDDK 1U01DK089571 |
PMID:24350770 PMID:22139914 |
nlx_151470 | SCR_006065 | Multi-Omics Profiling Expression Database | 2026-09-19 12:55:08 | 2 | ||||||
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EMAGE Gene Expression Database Resource Report Resource Website 10+ mentions |
EMAGE Gene Expression Database (RRID:SCR_005391) | EMAGE | atlas, data or information resource, data repository, database, service resource, storage service resource | A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without. | genetics, 3d model, anatomy, development, mouse morphology, molecular neuroanatomy resource, gene expression, in situ hybridization, immunohistochemistry, embryo, in situ reporter, embryonic mouse, optical projection tomography, confocal microscopy, annotation, pathway, gene association, protein, theiler stage, gene expression, embryology, dna, protein, protein-protein interaction, protein binding, gene, embryology, anatomy, genetics, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: HUDSEN Electronic Atlas of the Developing Human Brain is related to: eMouseAtlas is related to: eMouseAtlas is related to: HUDSEN Human Gene Expression Spatial Database is related to: aGEM is related to: Eurexpress is related to: Gene Expression Database is related to: Gene Ontology is related to: NIDDK Information Network (dkNET) is related to: GUDMAP Ontology |
MRC | PMID:19767607 | Except where noted, Creative Commons Attribution License, The community can contribute to this resource | biotools:emage, nif-0000-00080, r3d100010564 | https://bio.tools/emage, https://doi.org/10.17616/R3860B | SCR_005391 | Emage (e-Mouse Atlas of Gene Expression), e-Mouse Atlas of Gene Expression | 2026-09-19 12:55:08 | 25 |
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