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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VIB Compound Screening Facility Resource Report Resource Website |
VIB Compound Screening Facility (RRID:SCR_012256) | VIB CSF, VIB-CSF | service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Compound screening facility that has several drug-like compound collections available that amount to a total of about 74,000 compounds and a human siRNA library that targets almost 8,000 genes. State-of-the-art liquid handling systems and detection technologies are available for screening in-house or custom collections in 96- or 384-well plate format. The platform is compatible with biochemical assays, cell-based assays in a broad range of cellular systems and assays in the model plant Arabidopsis thaliana. Its core activities consist of managing the VIB screening collections, assisting researchers in assay development / automation and performing high-throughput screenings. After hit clustering and selection, the VIB-CSF team can contribute in structure-activity analysis, IC50 measurements, cytotoxicity analysis, secondary screening for hit validation and counter screening for specificity analysis. |
is listed by: ScienceExchange has parent organization: VIB; Flanders; Belgium has parent organization: Ghent University; Ghent; Belgium |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_11102 | SCR_012256 | VIB Compound Screening Facility (CSF) | 2026-08-15 11:31:18 | 0 | ||||||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-08-21 12:37:37 | 4535 | |||||
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | analysis service resource, data analysis service, production service resource, service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-08-20 09:27:05 | 114 | ||||||
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NLSdb: a database of nuclear localization signals Resource Report Resource Website 1+ mentions |
NLSdb: a database of nuclear localization signals (RRID:SCR_003273) | NLSdb | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree | nuclear localization signal, nuclear protein, nucleus, motif, predict, protein | has parent organization: Columbia University; New York; USA | NIGMS 1-P50-GM62413-01; NSF DBI-0131168 |
PMID:12520032 | Free for academic use, Acknowledgement requested, All others should inquire about a commercial license | nif-0000-03191 | http://cubic.bioc.columbia.edu/db/NLSdb/ | SCR_003273 | NLSdb - a database of nuclear localization signals | 2026-08-21 12:37:05 | 4 | ||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
European Molecular Biology Laboratory ; European Union FP6 ENFIN LSHG-CT-2005-518254; NHGRI P41 HG003751; NIGMS GM080223; NIGMS R01 GM100039; Ontario Research Fund |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-08-21 12:37:01 | 4810 | |||||
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Genoscope Resource Report Resource Website 100+ mentions |
Genoscope (RRID:SCR_002172) | Genoscope | institution | French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes. | environmental genomics, biocatalysis, environment, genomics, sequencing, bioinformatics, biodiversity, blast, blat, ggb, mage, metabolic, whole genome shotgun, chromosome 3, cdna, chromosome 14, alternative splicing, o��kopleura dioica, mutation, enzymatic cloning, screening, synteny, data set, genome, sequence, annotation, genome browser, FASEB list | has parent organization: CEA; Gif sur Yvette; France | Free, Freely available | Wikidata: Q3100800, ISNI: 0000 0004 0641 2997, grid.434728.e, nif-0000-20957 | https://ror.org/028pnqf58 | SCR_002172 | Genoscope - Centre National de S�quen�age, Genoscope - French National Sequencing Center, French National Sequencing Center, Genoscope - Centre National de Sequencage | 2026-08-21 12:36:38 | 165 | ||||||
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GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | data or information resource, data repository, database, service resource, storage service resource | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NCI U01 CA105417; NCRR U24 RR021760; NIAAA U01 AA014425; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIA R01 AG043930; NIDA P20 DA21131; NIGMS R01 GM123489 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-08-21 12:36:41 | 499 | |||||
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Aging Genes and Interventions Database Resource Report Resource Website 1+ mentions |
Aging Genes and Interventions Database (RRID:SCR_002701) | AGEID | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link. | allele, strain, gene function, phenotype, mutant, homolog, mutation, degeneration, gene, intervention, life-span |
is used by: Aging Portal is used by: NIF Data Federation has parent organization: University of Washington; Seattle; USA |
Aging, Age-related neurological disease, Neurological disease | Ellison Medical Foundation | PMID:12044961 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23326 | http://sageke.sciencemag.org/highlights/gidb/ | SCR_002701 | Aging Genes DB, Aging Genes Database, Genes/Interventions Database | 2026-08-21 12:36:50 | 2 | |||
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GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr, http://www.greenphyl.org/v3/, https://bio.tools/greenphyldb | SCR_002834 | 2026-08-21 12:36:51 | 20 | ||||||
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InParanoid: Eukaryotic Ortholog Groups Resource Report Resource Website 100+ mentions |
InParanoid: Eukaryotic Ortholog Groups (RRID:SCR_006801) | InParanoid | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded. | protein, ortholog, genome, drosophila pseudoobscura, duplication, entamoeba histolytica, escherichia colik12, eukaryotic, gasterosteus aculeatus, gene, aedes aegypti, apis mellifera, bos taurus, caenorhabditis remanei, candida glabrata, canis familiaris, ciona intestinalis, cryptococcus neoformans, debaromyces hansenii, dictyostelium discoideum, genomic, homolog, inparalog, kluyveromyces lactis, macaca mulatta, monodelphis domestica, orthology, oryza sativa, outparalog, proteome, tetraodon nigroviridis, xenopus tropicalis, blast, proteome, ortholog cluster, cluster, in-paralog, paralog, automatic clustering, genome comparison, FASEB list | has parent organization: Stockholm University; Stockholm; Sweden | Swedish Research Council ; Karolinska Institutet; Stockholm; Sweden ; Pfizer Corporation |
PMID:19892828 PMID:18055500 PMID:15608241 PMID:11743721 |
Acknowledgement requested | nif-0000-03024 | http://www.cgb.ki.se/inparanoid/ | SCR_006801 | Inparanoid eukaryotic ortholog database | 2026-08-21 12:38:03 | 189 | ||||
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DATFAP Resource Report Resource Website |
DATFAP (RRID:SCR_005413) | DATFAP | data or information resource, database | A database of transcription factors from 13 plant species, and PCR primers for around 90% of them. | homolog, sequence, transcription factor |
is listed by: OMICtools is related to: Gene Ontology |
PMID:18366738 | Free | OMICS_00552 | SCR_005413 | Database of transcription factors with alignments and primers | 2026-08-21 12:37:39 | 0 | ||||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 500+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | analysis service resource, data analysis service, production service resource, service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-08-21 12:38:04 | 524 | |||||
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Arabidopsis Gene Regulatory Information Server Resource Report Resource Website 50+ mentions |
Arabidopsis Gene Regulatory Information Server (RRID:SCR_006928) | AGRIS | data or information resource, database | An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB). | gene regulatory, gene, arabidopsis thaliana, promoter sequence, target gene, transcription factor, FASEB list |
is listed by: OMICtools has parent organization: Ohio State University; Ohio; USA |
NSF | PMID:21059685 PMID:16524982 PMID:12820902 |
Free, Acknowledgement requested | OMICS_00548, nif-0000-02540 | SCR_006928 | 2026-08-21 12:37:57 | 53 | ||||||
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AthaMap Resource Report Resource Website 50+ mentions |
AthaMap (RRID:SCR_006717) | data or information resource, database | Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. | gene, arabidopsis thaliana, binding site, genome, transcription factor, small rna binding site, small rna, rna, microrna, cis-regulatory element, post-transcriptional regulation, FASEB list |
is listed by: OMICtools is listed by: bio.tools has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
PMID:22800758 PMID:21177332 PMID:18842622 PMID:17148485 PMID:16922688 PMID:15980498 PMID:14681436 |
Free, Freely available | nif-0000-02583, biotools:athamap, OMICS_00549, nif-0000-20814, SCR_013106 | https://bio.tools/athamap | SCR_006717 | Arabidopsis thaliana Map | 2026-08-21 12:37:53 | 50 | ||||||
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The WWW Virtual Library: Model Organisms Resource Report Resource Website |
The WWW Virtual Library: Model Organisms (RRID:SCR_007007) | data or information resource, portal, topical portal | Catalog of internet resources relating to biological model organisms, and is part of the Biosciences area of the Virtual Library project. The main Model Organisms Library discussed in this website are: * E. coli (bacterium) * Yeasts (Saccharomyces cerevisiae, and other species) * Dictyostelium discoideum (slime mold) * Drosophila melanogaster (fruit fly) * Xenopus laevis (African clawed frog) Many aspects of biology are similar in most or all organisms, but it is frequently much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans! The most popular model organisms have strong advantages for experimental research, and become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information. | bacterium, cerevisiae, model organism, saccharomyces, s. cerevisiae, slime mold, xenopus, catalog, link aggregator | is listed by: 3DVC | nif-0000-20953 | SCR_007007 | VL | 2026-08-21 12:38:17 | 0 | |||||||||
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Biological General Repository for Interaction Datasets (BioGRID) Resource Report Resource Website 1000+ mentions |
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) | BioGRID | data or information resource, database | Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. | budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics, bio.tools, FASEB list |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: OMICtools is listed by: DataCite is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: Pathway Commons is related to: Cytoscape is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: PSICQUIC Registry is related to: PSI-MI is related to: NIH Data Sharing Repositories is related to: Agile Protein Interactomes DataServer is related to: Integrated Manually Extracted Annotation has parent organization: Princeton University; New Jersey; USA has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: University of Montreal; Quebec; Canada works with: IMEx - The International Molecular Exchange Consortium |
BBSRC ; Canadian Institutes of Health Research ; NCRR R01 RR024031; NHGRI HG02223; NIH Office of the Director R24 OD011194 |
PMID:23203989 PMID:21071413 PMID:16381927 PMID:12620108 |
Free, Freely available | nif-0000-00432, r3d100010350, OMICS_01901, biotools:the_grid | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://bio.tools/the_grid, https://doi.org/10.17616/R34C7G | SCR_007393 | , BioGRID, Biological General Repository for Interaction Datasets | 2026-08-21 12:38:08 | 2824 | ||||
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AraCyc Resource Report Resource Website 50+ mentions |
AraCyc (RRID:SCR_008109) | data or information resource, data repository, database, service resource, storage service resource | Curated species-specific database present at the Plant Metabolic Network. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways. | enzyme, gene, arabidopsis thaliana, biochemical, pathway, reaction, metabolism, metabolic pathway, data set, data analysis service, web service, FASEB list |
is used by: Arabidopsis Reactome is listed by: 3DVC has parent organization: Plant Metabolic Network |
NSF | PMID:12805578 PMID:15888675 |
The community can contribute to this resource | nif-0000-20811 | http://www.arabidopsis.org/biocyc/index.jsp, http://www.plantcyc.org | SCR_008109 | Arabidopsis enzymes and biochemical pathways database | 2026-08-21 12:38:34 | 69 | |||||
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DNAtraffic Resource Report Resource Website |
DNAtraffic (RRID:SCR_008886) | DNAtraffic | data or information resource, database | DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug. | dna, cell cycle, genome, nomenclature, ontology, structure, function, protein, chromatin remodeling, dna repair, damage response pathway, pathway, damage, drug, annotation, disease, dna network process, dna damage, gene sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Polish Academy of Sciences Warsaw; Warsaw; Poland |
Norwegian Financial Mechanism PNRF-143-AI-1/07; Polish Ministry of Science and Higher Education N N301 165835 |
PMID:22110027 | Free | biotools:dnatraffic, nlx_151312 | https://bio.tools/dnatraffic | SCR_008886 | DNAtraffic database | 2026-08-21 12:38:54 | 0 | ||||
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eSLDB - eukaryotic Subcellular Localization database Resource Report Resource Website 1+ mentions |
eSLDB - eukaryotic Subcellular Localization database (RRID:SCR_000052) | eSLDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions. | proteome, protein, homology | has parent organization: University of Bologna; Bologna; Italy | European Union VI Framework Programme | PMID:17108361 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02815 | SCR_000052 | eukaryotic Subcellular Localization database | 2026-08-21 12:36:06 | 1 | |||||
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STIFDB Resource Report Resource Website 10+ mentions |
STIFDB (RRID:SCR_002131) | STIFDB | data or information resource, database | Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method. | stress responsive, transcription factor, biotic, abiotic, gene, transcription factor binding site, promoter, stress, chromosome, blast |
is listed by: OMICtools has parent organization: Tata Institute of Fundamental Research; Mumbai; India |
PMID:23314754 PMID:19841686 |
Free, Freely Available | OMICS_01866 | SCR_002131 | Stress Responsive Transcription Factor Database | 2026-08-21 12:36:37 | 11 |
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