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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Cerebellar Development Transcriptome Database Resource Report Resource Website 1+ mentions |
Cerebellar Development Transcriptome Database (RRID:SCR_013096) | CDT-DB | atlas, data or information resource, database | Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. | gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development |
is related to: Gene Ontology is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
Brain development, Brain disorder | INCF Japan Node ; Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:18603407 | To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. | nif-0000-00008 | SCR_013096 | 2026-09-12 01:02:09 | 1 | |||||
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doRiNA Resource Report Resource Website 10+ mentions |
doRiNA (RRID:SCR_013222) | doRiNA | data or information resource, database | In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions. | binding site, rna binding protein, microrna, post-transcription, rna, gene, genome, mammal, population variation, gene expression, transcript, regulator, protein, binding |
is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
MDC Systems Biology Network ; BMBF ; Senate of Berlin; Berlin; Germany ; DFG |
PMID:22086949 | nlx_151321, r3d100011087 | SCR_013222 | 2026-09-12 01:02:10 | 15 | |||||||
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PLAN2L Resource Report Resource Website |
PLAN2L (RRID:SCR_013346) | PLAN2L | data or information resource, database, service resource | A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. | text mining, bio-entity relation extraction, literature, information extraction, cell cycle, regulation, protein interaction, cellular location, flowering, leave, root, seed, gene, normalization, interaction, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:19520768 | OMICS_01192, biotools:plan2l | https://bio.tools/plan2l | SCR_013346 | PLAN2L: Plant Annotation to Literature, Plant annotation to literature | 2026-09-12 01:02:11 | 0 | ||||||
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aGEM Resource Report Resource Website 10+ mentions |
aGEM (RRID:SCR_013349) | aGEM | data or information resource, database | Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, anatomy, gene expression, anatomical structure, developmental stage, functional genomics, genomics |
is related to: EMAGE Gene Expression Database is related to: Gene Expression Database is related to: Gene Expression Nervous System Atlas is related to: BioGPS: The Gene Portal Hub is related to: Allen Mouse Brain Reference Atlas is related to: Eurexpress is related to: HUDSEN is related to: The Human Protein Atlas is related to: OMIM is related to: KEGG has parent organization: Autonomous University of Madrid; Madrid; Spain |
National Institute for Bioinformatics ; AMIT Programme CDTI CEN-20101014; RESOLVE UE CE:FP7-202047; Ministerio de Ciencia e Innovacion BIO2010-16566; Biostruct-X FP7-Infrastructures-2011-1; Centrosoma 3D CSD2006-00023 |
PMID:22106336 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152022 | SCR_013349 | anatomic Gene Expression Mapping | 2026-09-12 01:02:11 | 12 | |||||
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Drosophila melanogaster Exon Database Resource Report Resource Website 1+ mentions |
Drosophila melanogaster Exon Database (RRID:SCR_013441) | DEDB | data or information resource, database | Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. | exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast |
is listed by: OMICtools is related to: FlyBase has parent organization: National University of Singapore; Singapore; Singapore |
Agency for Science Technology and Research | PMID:15581431 | nif-0000-21118, OMICS_01894 | SCR_013441 | DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database | 2026-09-12 01:02:11 | 2 | ||||||
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RARTF Resource Report Resource Website 1+ mentions |
RARTF (RRID:SCR_013457) | RARTF | data or information resource, database | Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available. | transcription factor, protein, gene, microarray, expression profile |
is listed by: OMICtools is related to: InterProScan |
PMID:16769687 | Free | OMICS_00562 | SCR_013457 | RARTF: RIKEN Arabidopsis Transcription Factor database, RIKEN Arabidopsis Transcription Factor database | 2026-09-12 01:02:12 | 2 | ||||||
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Genes, Genome Features and Maps Resource Report Resource Website 1+ mentions |
Genes, Genome Features and Maps (RRID:SCR_017524) | data or information resource, database | Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models. | Data, mouse, gene, DNA, segment, cytogenetic, marker, MGI, genome, feature, sequenced, genomic, map, expression, disease, model | Free, Freely available | SCR_017524 | 2026-09-12 01:02:18 | 6 | |||||||||||
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miRanda Resource Report Resource Website 100+ mentions |
miRanda (RRID:SCR_017496) | data or information resource, database, service resource | Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list | is listed by: SoftCite | Alfred W. Bressler Scholars Endowment Fund ; Atlantic Philanthropies ; NIGMS |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.microrna.org/microrna/home.do | SCR_017496 | MicroRNA.org. microrna.org | 2026-09-12 01:02:18 | 281 | ||||||
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IST Online Resource Report Resource Website 10+ mentions |
IST Online (RRID:SCR_018794) | data or information resource, database, service resource | Database by Medisapiens Ltd. as fully integrated and annotated human gene expression data source. All genes are comparable across all samples. Provides data analysis options using database of human transcriptome. | Human gene, gene expression data, data, gene expression, gene, human transcriptome, Medisapiens Ltd. | Restricted | SCR_018794 | 2026-09-12 01:02:19 | 16 | |||||||||||
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C. elegans RNAi Collection (Ahringer) Resource Report Resource Website 10+ mentions |
C. elegans RNAi Collection (Ahringer) (RRID:SCR_017064) | data or information resource, database | C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies. | Source BioScience Ltd, data, collection, bacterial, strain, Caenorhabditis elegans, RNA, interference, RNAi, gene, function, analysis, feeding, library | has parent organization: University of Cambridge; Cambridge; United Kingdom | Howard Hughes Medical Institute Predoctoral Fellow- ship ; Wellcome Trust Senior Research Fellowship |
PMID:12828945 | Available for purchase | SCR_017064 | 2026-09-12 01:02:17 | 16 | ||||||||
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VGNC Resource Report Resource Website 10+ mentions |
VGNC (RRID:SCR_017514) | data or information resource, database, service resource | Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs. | Vertebrate, gene, nomenclature, data, symbol | is related to: HGNC | NHGRI U24 HG003345; Wellcome Trust |
Free, Freely available | SCR_017514 | Vertebrate Gene Nomenclature Committee | 2026-09-12 01:02:18 | 14 | ||||||||
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miRWalk Resource Report Resource Website 1000+ mentions |
miRWalk (RRID:SCR_016509) | data or information resource, database | Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets. | microRNA, target, interaction, pair, binding, site, sequence, gene, data, FASEB list | is listed by: OMICtools | PMID:26226356 | Free, Available for download, Freely available | SCR_016509 | 2026-09-12 01:02:17 | 1741 | |||||||||
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Kidney Interactive Transcriptomics Resource Report Resource Website 50+ mentions |
Kidney Interactive Transcriptomics (RRID:SCR_017209) | KIT | analysis service resource, data or information resource, production service resource, service resource | Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website. | Analyzer, kidney, single, cell, dataset, gene, expression, mouse, human, organoid | Free, Freely available | https://www.rebuildingakidney.org/ | SCR_017209 | 2026-09-12 01:02:17 | 99 | |||||||||
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ALZPEDIA Resource Report Resource Website 1+ mentions |
ALZPEDIA (RRID:SCR_017548) | AlzPedia | data or information resource, database | Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge. | Summary, gene, protein, pathophysiology, Alzheimer, neurodegenerative, disorder | is related to: Alzheimer's Research Forum | Free, Freely available | SCR_017548 | 2026-09-12 01:02:18 | 3 | |||||||||
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PlantGSEA Resource Report Resource Website 10+ mentions |
PlantGSEA (RRID:SCR_016866) | PlantGSEA | analysis service resource, data analysis service, production service resource, service resource | Websever for gene set enrichment analysis of plants. Used for interpreting biological meaning of a list of genes by computing the overlaps with various previously defined gene sets. | gene, set, enrichement, analysis, plant | Ministry of Education of China ; Ministry of Science and Technology of China |
DOI:10.1093/nar/gkt281 | SCR_016866 | The Plant GeneSet Enrichment Analysis Toolkit, Plant GeneSet Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-09-12 01:02:17 | 18 | ||||||||
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Database of genes related to Repeat Expansion Diseases Resource Report Resource Website 1+ mentions |
Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) | DRED | data or information resource, database, service resource | Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest. | Gene, repeat expansion disease, unstable tandem repeat, abnormal repeat expansion, data |
works with: OMIM works with: NCBI works with: Ensembl |
Repeat Expansion Diseases | Free, Freely available | SCR_018086 | Database of genes related to Repeat Expansion Diseases | 2026-09-12 01:02:18 | 1 | |||||||
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CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software resource, software toolkit | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-09-12 01:02:23 | 31 | ||||||||
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EM-DECODER Resource Report Resource Website 1+ mentions |
EM-DECODER (RRID:SCR_000023) | EM-DECODER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program. | gene, genetic, genomic |
is listed by: Genetic Analysis Software has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154297 | SCR_000023 | 2026-09-12 01:02:22 | 1 | ||||||||
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Genetics of Kidneys in Diabetes Resource Report Resource Website |
Genetics of Kidneys in Diabetes (RRID:SCR_000133) | GoKinD, Go KinD | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Collect, store, and distribute genetic samples from cases and controls of type 1 diabetes and diabetic nephropathy for investigator-driven research into the genetic basis of diabetic nephropathy. As the risk of kidney complications in type 1 diabetes appears to have a considerable genetic component, this study assembled a large data resource for researchers attempting to identify causative genetic variants. The types of data collected allowed traditional case-control testing, a rapid and often powerful approach, and family-based analysis, a robust approach that is not influenced by population substructure. | clinical, genetics, genetic variant, gene, data set |
is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) has parent organization: George Washington University; Washington D.C.; USA |
Type 1 diabetes, Diabetes, Diabetic nephropathy, Kidney disease | JDRF ; NIH |
PMID:16775037 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152764 | http://www.gokind.org/access | SCR_000133 | Genetics of Kidneys in Diabetes (GoKinD) Study, Genetics of Kidneys in Diabetes Study | 2026-09-12 01:02:22 | 0 | |||
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HAPSCOPE Resource Report Resource Website |
HAPSCOPE (RRID:SCR_000838) | HAPSCOPE | software application, software resource | Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | PMID:12466546 | nlx_154393 | SCR_000838 | 2026-09-12 01:02:24 | 0 |
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