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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | software application, data analysis software, source code, software resource, data processing software, simulation software | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-07-28 09:40:44 | 126 | |||
|
Xenbase Resource Report Resource Website 100+ mentions |
Xenbase (RRID:SCR_003280) | XenBase | service resource, data or information resource, data repository, image repository, database, storage service resource | Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics. | molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard, bio.tools, FASEB list, RRID Community Authority |
is listed by: OMICtools is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of Calgary; Alberta; Canada is parent organization of: Xenopus Anatomy Ontology |
NICHD R01 HD045776; NICHD P41 HD064556 |
PMID:23125366 PMID:19884130 PMID:36755307 |
Free, Available for download, Freely available | biotools:xenbase, OMICS_01665, nif-0000-01286, r3d100010279 | http://www.xenbase.org/entry/, https://bio.tools/xenbase, https://doi.org/10.17616/R3MP4S | SCR_003280 | Xenbase: Xenopus laevis and tropicalis biology and genomics resource | 2026-07-28 09:40:39 | 446 | ||||
|
genomation Resource Report Resource Website 50+ mentions |
genomation (RRID:SCR_003435) | genomation | software application, data analysis software, software resource, data processing software, software toolkit | Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters. | genome, genomic interval, genomic feature analysis, GRanges objects, annotate given regions, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:25417204 | Free, Available for download, Freely available | biotools:genomation, OMICS_02306 | https://github.com/al2na/genomation, https://github.com/BIMSBbioinfo/genomation, https://bio.tools/genomation | http://al2na.github.io/genomation/ | SCR_003435 | 2026-07-28 09:40:47 | 58 | |||||
|
Phospho.ELM Resource Report Resource Website 10+ mentions |
Phospho.ELM (RRID:SCR_001109) | data or information resource, database | Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database. | eukaryotic protein, phosphorylation site, database, curation, bio.tools, FASEB list |
uses: UniProt is listed by: bio.tools is listed by: Debian has parent organization: University of Dundee; Scotland; United Kingdom |
PMID:17962309 | Publicly available | nif-0000-03278, biotools:phosphoelm | https://bio.tools/phosphoelm | SCR_001109 | 2026-07-28 09:40:11 | 40 | |||||||
|
A Classification of Mobile genetic Elements Resource Report Resource Website 10+ mentions |
A Classification of Mobile genetic Elements (RRID:SCR_001694) | ACLAME | data or information resource, database | A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME. | mobile genetic element, phage genome, plasmid, virus, prophage, transposon, protein, gene, classification, data analysis service, prophage prediction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Free University of Brussels; Brussels; Belgium is parent organization of: MeGO |
ESTEC contract ESTEC 16370/02/NL/CK | PMID:19933762 PMID:14681355 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02533, OMICS_01528, biotools:aclame | https://bio.tools/aclame | SCR_001694 | ACLAME: A CLAssification of Mobile genetic Elements | 2026-07-28 09:40:15 | 31 | ||||
|
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 | 2026-07-28 09:40:33 | 14 | ||||
|
BISC Resource Report Resource Website 10+ mentions |
BISC (RRID:SCR_002064) | BISC | data or information resource, database | A protein-protein interaction (PPI) database intending to bridge between the two communities most active in their characterization: structural biology and functional genomics researchers. It offers users access to binary subcomplexes, (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD. Selected web services are available to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein-protein interaction, binary subcomplex, bio.tools |
is listed by: OMICtools is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA |
PMID:21081561 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01902, biotools:bisc | https://bio.tools/bisc | SCR_002064 | BInary SubComplex Database | 2026-07-28 09:40:20 | 14 | |||||
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The Alternatve Splicing Database Resource Report Resource Website 1+ mentions |
The Alternatve Splicing Database (RRID:SCR_001883) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale. The current release of the human genome consists of: 16715 genes, 14101 have more than one splice isoform, with an average of 5.6 splice patterns per gene. 10831 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the mouse genome consists of: 16491 genes, 13028 have more than one splice isoform, with an average of 4 splice patterns per gene. 6011 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the rat genome consists of: 10424 genes, 6344 have more than one splice isoform, with an average of 2.6 splice patterns per gene. 1250 transcripts are annotated as full length with a transcription start site and a poly(A). Sponsors: The ASTD project at EBI is supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238). It was also supported by the ASD grant from the EC (QLRT-CT-2001-02062) until November 2005 and the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007. | exon, exon splice site, gene, gene structure, alternative splicing, human genome, intron, intron splice site, mouse genome, nucleotide sequence database, rat genome, splice isoform, transcript, transcription, transcription diversity, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:19059335 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02579, biotools:astd | https://bio.tools/astd | SCR_001883 | ASTD | 2026-07-28 09:40:17 | 5 | ||||||
|
CHEBI Resource Report Resource Website 100+ mentions |
CHEBI (RRID:SCR_002088) | ChEBI | data or information resource, database | Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. | complex, conformer, ion, ion pair, isotope, molecular entity, molecule, radical, radical ion, small molecule, obo, gold standard, biochemistry, metabolomics, bio.tools |
uses: IUPAC uses: Nomenclature Committee of IUBMB is used by: Open PHACTS is used by: Ultimate Rough Aggregation of Metabolic Map is used by: RHEA is used by: GEROprotectors is used by: SwissLipids is listed by: OBO is listed by: BioPortal is listed by: NIF Data Federation is listed by: SourceForge is listed by: bio.tools is listed by: Debian is related to: Pathway Commons is related to: Integrated Manually Extracted Annotation has parent organization: European Bioinformatics Institute is parent organization of: Physico-Chemical Process is parent organization of: Physico-Chemical Methods and Properties works with: MiMeDB |
BBSRC BB/G022747/1 | PMID:19854951 PMID:19496059 PMID:17932057 |
Freely available | nif-0000-02655, biotools:chebi, r3d100012626 | http://bioportal.bioontology.org/ontologies/1007, http://www.obofoundry.org/cgi-bin/detail.cgi?id=chebi, ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo, http://chebi.wiki.sourceforge.net/, https://bio.tools/chebi | http://www.ebi.ac.uk/chebi/ | SCR_002088 | CHEBI, Chemical Entities of Biological Interest | 2026-07-28 09:40:33 | 126 | |||
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FlyFactorSurvey Resource Report Resource Website 10+ mentions |
FlyFactorSurvey (RRID:SCR_002113) | FlyFactorSurvey | data or information resource, database | Database of Drosophila transcription factor DNA binding specificity using the bacterial one-hybrid method, DNase I or SELEX methods. The database provides community access to recognition motifs and position weight matrices for transcription factors (TFs), including many unpublished motifs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within the database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. This database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis-regulatory sequences. | transcription factor, motif, cis-regulatory module, transcription factor binding site, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Massachusetts Medical School; Massachusetts; USA |
NHGRI 1R01HG005287-01A1 | PMID:21097781 | Free, Available for download, Freely available | biotools:flyfactorsurvey, OMICS_01879 | https://bio.tools/flyfactorsurvey | SCR_002113 | 2026-07-28 09:40:21 | 25 | |||||
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BioNumbers Resource Report Resource Website 10+ mentions |
BioNumbers (RRID:SCR_002782) | BioNumbers | data or information resource, database | Database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers. While always of importance to biologists, having numbers in hand is becoming increasingly critical for experimenting, modeling, and analyzing biological systems. BioNumbers was motivated by an appreciation of how long it can take to find even the simplest number in the vast biological literature. All numbers are taken directly from a literature source and that reference is provided with the number. BioNumbers is designed to be highly searchable and queries can be performed by keywords or browsed by menus. BioNumbers is a collaborative community platform where registered users can add content and make comments on existing data. All new entries and commentary are curated to maintain high quality. | biological, biological system, bionumber, molecular biology, number, photosynthesis, quantitative, sporulation, quantitative analysis, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Integrated Manually Extracted Annotation has parent organization: Harvard University; Cambridge; United States |
Harvard University; Massachusetts; USA ; Weizmann Institute of Science; Rehovot; Israel |
PMID:19854939 | Free, Freely available | nif-0000-24396, biotools:bionumbers | https://bio.tools/bionumbers | SCR_002782 | BioNumbers: The Database of Useful Biological Numbers | 2026-07-28 09:40:40 | 48 | ||||
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CoryneRegNet Resource Report Resource Website 10+ mentions |
CoryneRegNet (RRID:SCR_002255) | CoryneRegNet | data or information resource, database | Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. It generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure. | gene, regulatory network, transcription factor, interaction, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Cytoscape has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
PMID:22080556 PMID:19498379 PMID:18426593 PMID:17986320 PMID:17229482 PMID:16478536 |
Free, Freely available | biotools:coryneregnet, nif-0000-02689, OMICS_01858 | https://bio.tools/coryneregnet | SCR_002255 | 2026-07-28 09:40:23 | 17 | ||||||
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Zebrafish Information Network (ZFIN) Resource Report Resource Website 500+ mentions |
Zebrafish Information Network (ZFIN) (RRID:SCR_002560) | ZFIN | data or information resource, database | Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases. | expression, gene, anatomy, development, disease, genomic, model, molecular, mutant, neuronal, organism, phenotype, physiological, synteny, zebrafish, gene expression, genome sequence, molecular neuroanatomy resource, genotype, anatomical structure, publication, genome, image collection, gold standard, bio.tools, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: Morpholino Database is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: InterMOD is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Phenoscape Knowledgebase is related to: MONARCH Initiative is related to: Bgee: dataBase for Gene Expression Evolution is related to: NIH Data Sharing Repositories is related to: HomoloGene is related to: Zebrafish International Resource Center is related to: Integrated Manually Extracted Annotation is related to: Zebrafish Genome Project has parent organization: University of Oregon; Oregon; USA is parent organization of: ZFIN Antibody Database is parent organization of: Zebrafish Anatomical Ontology is parent organization of: ZFIN Protocol Wiki is parent organization of: ZFIN Antibody Wiki is organization facet of: Alliance of Genome Resources |
NHGRI P41 HG002659; NHGRI R01 HG004834 |
PMID:23074187 PMID:21036866 PMID:16381936 |
Free, Available for download, Freely available | OMICS_01666, nif-0000-21427, biotools:zfin, r3d100010421, SCR_017504 | http://zfin.org/ZFIN/misc_html/tips.html#newrecord, https://wiki.zfin.org/display/general/ZFIN+Data+Submissions, https://bio.tools/zfin, https://doi.org/10.17616/R3CK5Z | SCR_002560 | Zebrafish Database, The Zebrafish Model Organism Database, Zebra Model Organism Database, ZebraFish Information Network, ZFIN | 2026-07-28 09:40:28 | 898 | ||||
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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 | 2026-07-28 09:40:23 | 1 | ||||
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T3DB Resource Report Resource Website 10+ mentions |
T3DB (RRID:SCR_002672) | T3DB | data or information resource, database | Database that combines detailed toxin data with comprehensive toxin target information. The database currently houses 3,053 toxins described by 32,276 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 1,670 corresponding toxin target records. Altogether there are 37,084 toxin, toxin target associations. (March 2014) Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5,454 sources sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches | toxicology, toxin, pollutant, pesticide, drug, food, gene-drug, interaction, gene, phenotype, mechanism, bio.tools |
is used by: NIF Data Federation is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: FMA has parent organization: University of Alberta; Alberta; Canada |
Alberta Advanced Education and Technology ; Canadian Institutes of Health Research ; Genome Alberta ; Genome Canada |
PMID:19897546 | Free, Available for download, Freely available | r3d100012189, nif-0000-22933, biotools:t3db, OMICS_01592 | https://bio.tools/t3db, https://doi.org/10.17616/R3VM0R | SCR_002672 | Toxin-Target Database, Toxin Toxin-Target Database, Toxin and Toxin Target Database, Toxin, Toxin Toxin Target Database | 2026-07-28 09:40:29 | 24 | ||||
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TcoF Resource Report Resource Website 10+ mentions |
TcoF (RRID:SCR_002158) | TcoF | data or information resource, database | Database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors). | protein, regulation, transcription, transcription factor, transcription co-factor, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:20965969 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tcof-db, OMICS_01865 | https://bio.tools/tcof-db | SCR_002158 | Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins, TcoF-DB, TcoF - Dragon database of transcription co-factors and transcription factor interacting proteins | 2026-07-28 09:40:21 | 10 | |||||
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HINT Resource Report Resource Website 100+ mentions |
HINT (RRID:SCR_002762) | HINT | data or information resource, database | A database of high-quality protein-protein interactions in different organisms. | protein-protein interaction, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Cornell University; New York; USA |
PMID:22846459 | Free, Freely available, Available for download | OMICS_02898, biotools:hint | https://bio.tools/hint | SCR_002762 | High-quality INTeractomes | 2026-07-28 09:40:31 | 306 | |||||
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Entrez Gene Resource Report Resource Website 1000+ mentions |
Entrez Gene (RRID:SCR_002473) | NCBI_Gene, NCBI Genen NCBI Entrez | data or information resource, database | Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available. | gene, gene expression, gene location, gene map, gene prediction, genome, genome sequence analysis, phenotype, nomenclature, gene mapping, protein, genetic code, function, annotation, gold standard, bio.tools |
is used by: Animal QTLdb is used by: NIF Data Federation is used by: LIPID MAPS Proteome Database is used by: DisGeNET is used by: Nowomics is used by: Cytokine Registry is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Vesiclepedia is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Rat Gene Symbol Tracker is related to: Gene Reference into Function is related to: Integrated Molecular Interaction Database is related to: Biomine is related to: SEGS is related to: STOP is related to: Coremine Medical is related to: Consensus CDS is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: Array Information Library Universal Navigator is related to: biomaRt has parent organization: NCBI works with: Open Regulatory Annotation Database |
PMID:17148475 PMID:21115458 |
Free, Freely available | nif-0000-02801, biotools:entrez_gene, OMICS_01651, r3d100010650 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene, http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene, https://bio.tools/entrez_gene, https://doi.org/10.17616/R3603S | SCR_002473 | NCBI Gene, Gene - Gene mapped phenotypes, Gene - Gene and mapped phenotypes, Gene Database, GeneID | 2026-07-28 09:40:37 | 2830 | |||||
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DBTSS: Database of Transcriptional Start Sites Resource Report Resource Website 100+ mentions |
DBTSS: Database of Transcriptional Start Sites (RRID:SCR_002354) | DBTSS | data or information resource, database | Database of transcriptional start sites (TSSs) representing exact positions in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. A major part of human adult and embryonic tissues are covered. DBTSS contains 491 million TSS tag sequences collected from a total of 20 tissues and 7 cell cultures. Also integrated is generated RNA-seq data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. Also included is external epigenomic data, such as chromatin map of the ENCODE project. They associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions. | cdna, cdna library, transcriptional start site, transcriptome, transcriptome analysis, tss-seq, genome, adult human, embryonic, cell, rna-seq, subcellular, rna, chip seq data, histone modification, rna polymerase ii, transcriptional regulatory factor, cell line, single nucleotide variation, regulatory region, genetic valuation, transcriptional regulation, bio.tools, FASEB list |
is used by: Transcriptional Regulatory Element Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:22086958 PMID:19910371 PMID:17942421 PMID:16381981 PMID:14681363 PMID:11752328 |
nif-0000-02738, biotools:dbtss, OMICS_01860 | https://bio.tools/dbtss | SCR_002354 | DBTSS: Database of Transcriptional Start Sites, DataBase of Transcriptional Start Sites | 2026-07-28 09:40:24 | 124 | |||||
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RESID Resource Report Resource Website 10+ mentions |
RESID (RRID:SCR_003505) | RESID | data or information resource, database | A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. It provides: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries. | protein cross-link, protein modification, protein structure, protein, structure, annotation, amino-terminal, carboxyl-terminal, peptide chain cross-link, post-translational modification, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:15174122 PMID:12520062 |
nif-0000-03400, r3d100000023, biotools:resid | https://bio.tools/resid, https://doi.org/10.17616/R3Z59M | http://www.ebi.ac.uk/RESID/ | SCR_003505 | RESID Database at the EBI, RESID Database at PIR, RESID Database of Protein Modifications, RESID Database | 2026-07-28 09:40:43 | 10 |
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