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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AthaMap Resource Report Resource Website 10+ 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 | 2026-02-11 10:57:23 | 48 | ||||||
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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 | 2026-02-11 10:55:58 | 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 | 2026-02-11 10:56:23 | 10 | ||||||
|
WikiPathways Resource Report Resource Website 1000+ mentions |
WikiPathways (RRID:SCR_002134) | service resource, data or information resource, database | Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community. | database, knowledge environment resource, image, web service, biological pathway, diagram description, reference, pathway, FASEB list |
is used by: NIF Data Federation is used by: Open PHACTS is related to: PharmGKB is related to: Reactome is related to: NetPath is related to: ConsensusPathDB is related to: NCBI BioSystems Database is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of California at San Francisco; California; USA has parent organization: Maastricht University; Maastricht; Netherlands |
NIH ; Netherlands Bioinformatics Centre ; Google Summer of Code program ; NWO - Netherlands Organization for Scientific Research ; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:22096230 PMID:18651794 |
Free, Freely available | nif-0000-20925 | SCR_002134 | Wiki Pathways | 2026-02-11 10:56:23 | 1696 | ||||||
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MetaCrop Resource Report Resource Website 1+ mentions |
MetaCrop (RRID:SCR_003100) | MetaCrop | data or information resource, database | Database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models. It contains manually curated, highly detailed information about metabolic pathways in crop plants, including pathway diagrams, reactions, locations, transport processes, reaction kinetics, taxonomy and literature. It contains information about seven major crop plants with high agronomical importance and two model plants. | metabolism, kinetic, enzyme, crop, pathway, substance, conversion, carbohydrate, lipid, cofactor, energy, nucleotide, amino acid, web service |
is listed by: re3data.org is related to: SBML has parent organization: Leibniz Institute of Plant Genetics and Crop Plant Research; Saxony-Anhalt; Germany |
PMID:22086948 PMID:17933764 PMID:20375443 |
Free, Freely available | nif-0000-03113, r3d100010123 | https://doi.org/10.17616/R33G6T | SCR_003100 | 2026-02-11 10:56:41 | 7 | ||||||
|
PLAN2L Resource Report Resource Website |
PLAN2L (RRID:SCR_013346) | PLAN2L | service resource, data or information resource, database | 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 | 2026-02-11 10:58:44 | 0 | ||||||
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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 | 2026-02-11 10:58:46 | 2 | ||||||
|
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 | 2026-02-11 10:57:58 | 0 | ||||
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EID: Exon-Intron Database Resource Report Resource Website 10+ mentions |
EID: Exon-Intron Database (RRID:SCR_002469) | EID | data or information resource, data set | Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. | eukaryote genome, exon, exon-intro, gene structure, genome splicing, intron, ortholog, fasta, gene, protein-coding gene, splice, motif, gene prediction, structure, coding region |
is listed by: OMICtools has parent organization: University of Toledo; Ohio; USA |
PMID:16772261 PMID:10592221 |
Free, Available for download, Freely available | OMICS_01886, nif-0000-02793 | http://www.utoledo.edu/med/depts/bioinfo/database.html | http://www.meduohio.edu/bioinfo/eid/, http://mcb.harvard.edu/gilbert/EID | SCR_002469 | The Exon-Intron Database, Exon-Intron Database | 2026-02-11 10:56:28 | 11 | ||||
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Mikado Resource Report Resource Website 50+ mentions |
Mikado (RRID:SCR_016159) | software resource, source code | Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus. | annotation, rna-seq, genomics, transcriptomics | is related to: Portcullis | BBSRC BB/J004669/1; BBSRC BB/J010375/1; BBSRC BB/CSP17270/1; BBSRC BB/CCG1720/1 |
DOI:10.1101/216994 | Free, Available for download | http://mikado.readthedocs.io/ | SCR_016159 | 2026-02-11 10:59:28 | 82 | |||||||
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Saskatoon Arabidopsis T-DNA mutant population SK Collection Resource Report Resource Website 1+ mentions |
Saskatoon Arabidopsis T-DNA mutant population SK Collection (RRID:SCR_004939) | SK-FST | biomaterial supply resource, material resource | Population of almost 50,000 activation tagged Arabidopsis thaliana lines that have been archived as individual lines to the T3 generation. The population is an excellent tool for both reverse and forward genetic screens and has been used successfully to identify a number of novel mutants. Flanking sequence tags (FST) have been generated and mapped for 15,507 lines to enable further application of the population, while providing a clear distribution of T-DNA insertions across the genome. The population is being screened for a number of biochemical and developmental phenotypes. The population provides an additional tool for plant researcher's to assist with determining gene function for the many as yet uncharacterized genes annotated within the Arabidopsis genome sequence. The presence of enhancer elements on the inserted T-DNA element (pSKI015) allows both knock-out and dominant activation phenotypes to be identified for traits of interest. | arabidopsis thaliana, genetics, mutant, biochemical, developmental, phenotype, gene function, flanking sequence tag, trait, t-dna | is related to: TAIR | AAFC Canadian Crop Genomics Initiative ; NSERC |
PMID:19646253 PMID:19347643 |
Free, Public | nlx_91019 | SCR_004939 | SK population | 2026-02-07 02:14:18 | 3 | |||||
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PhosPhAt Resource Report Resource Website 50+ mentions |
PhosPhAt (RRID:SCR_003332) | PhosPhAt | production service resource, data repository, data or information resource, database, storage service resource, data analysis service, service resource, analysis service resource | Database containing information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given. The PhosPhAt service has a built-in plant specific phosphorylation site predictor trained on the experimental dataset for Serine, threonine and tyrosine phosphorylation (pSer, pThr, pTyr). Protein sequences or Arabidopsis AGI gene identifier can be submitted to the predictor. Users and researchers are encouraged to assist in keeping the database current by submitting either published data or unpublished data (MS/MS data required). | phosphorylation, peptide, function, mass spectrometry, kinase, serine, threonine, tyrosine, phosphoprotein, phosphopeptide, tryptic phosphopeptide, serine phosphosite, threonine phosphosite, tyrosine phosphosite, FASEB list | has parent organization: University of Hohenheim; Baden-Wurttemberg; Germany | PMID:23172287 PMID:19880383 PMID:17984086 |
Free, Freely available | nif-0000-03277 | http://phosphat.mpimp-golm.mpg.de/app.html | SCR_003332 | Arabidopsis Protein Phosphorylation Site Database | 2026-02-11 10:56:43 | 57 | |||||
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GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | production service resource, software resource, web service, data access protocol, data analysis service, service resource, analysis service resource | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-02-11 10:57:27 | 348 | ||||
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GeneMerge Resource Report Resource Website 10+ mentions |
GeneMerge (RRID:SCR_005744) | GeneMerge | software application, production service resource, software resource, data analysis service, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Harvard University; Cambridge; United States |
PMID:12724301 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149203 | http://genemerge.cbcb.umd.edu/ | SCR_005744 | 2026-02-11 10:57:13 | 26 | ||||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | software resource, software application, data processing software, data analysis software | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-02-11 10:57:56 | 8 | |||||
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TAIR Resource Report Resource Website 5000+ mentions |
TAIR (RRID:SCR_004618) | TAIR, AGI LocusCode | data or information resource, database | Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided. | genetic, molecular biology, gene, genome, structure, product, metabolism, gene expression, dna, seed stock, genome map, genetic marker, physical marker, genome sequence, gene product, blast, experimental protocol, gold standard |
is used by: NIF Data Federation is listed by: OMICtools is listed by: re3data.org is listed by: DataCite is related to: AmiGO is related to: Saskatoon Arabidopsis T-DNA mutant population SK Collection is related to: CLENCH has parent organization: Carnegie Institution for Science is parent organization of: TAIR Keyword Browser is parent organization of: PubSearch |
NSF DBI-0850219; corporate and nonprofit organizations |
PMID:22140109 PMID:17986450 PMID:12444417 PMID:12519987 PMID:18287693 |
r3d100010185, nlx_61477, OMICS_01662 | https://doi.org/10.17616/R3QW21 | SCR_004618 | AGI LocusCode, The Arabidopsis Information Resource | 2026-02-11 10:57:00 | 7421 | |||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | data repository, data or information resource, database, d spatial image, image collection, service resource, storage service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-02-11 10:57:48 | 7 | |||||
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PubSearch Resource Report Resource Website 1+ mentions |
PubSearch (RRID:SCR_005830) | PubSearch | software resource, service resource, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotate, editor, literature curation tool, literature, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: TAIR has parent organization: Stanford University; Stanford; California |
NHGRI R01HG02728 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149338 | SCR_005830 | 2026-02-11 10:57:10 | 1 | |||||||
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mirEX Resource Report Resource Website 10+ mentions |
mirEX (RRID:SCR_006060) | mirEX | production service resource, data or information resource, database, atlas, data analysis service, service resource, analysis service resource | mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window. | microrna gene expression, microrna, gene expression, gene, organ, developmental stage, plant, seed, seedling, mature plant, pri-mirna, biotic stress, abiotic stress, organ formation, primer, cdna | has parent organization: Adam Mickiewicz University in Poznan; Poznan; Poland | Foundation for Polish Science ; European Union ; Regional Development Fund MPD 2010/3; Polish Ministry of Science and Higher Education 3011/B/P01/2009/37 |
PMID:22013167 | nlx_151462 | http://bioinfo.amu.edu.pl/mirex | SCR_006060 | 2026-02-11 10:57:15 | 10 | ||||||
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CSHL - Hannon Lab Resource Report Resource Website 50+ mentions |
CSHL - Hannon Lab (RRID:SCR_005982) | Hannon Lab | organization portal, portal, laboratory portal, data or information resource | The Hannon laboratory comprises a broad spectrum of programs in small RNA biology, mammalian genetics and genomics. We study RNAi and related pathways in a wide variety of organisms to extract common themes that define both the mechanisms by which small RNAs act and the biological processes which they impact. Currently, we focus on microRNAs, endogenous siRNAs and piRNAs and their roles in gene regulation, cancer biology, stem cell biology and in defense of the genome against transposons. In collaboration with Steve Elledge (Harvard) and Scott Lowe (CSHL), we develop genome-wide shRNA tools for RNAi-based genetics in mammalian cells, and we are now producing similar collections of artificial microRNAs for Arabidopsis with Detlef Weigel (MPI), Dick McCombie (CSHL) and Rob Martienssen (CSHL) as part of the 2010 project (see 2010.cshl.edu). Our genomic efforts include the application of RNAi-based genetic screens to cancer biology and stem cells. We also make heavy use of next generation sequencing methodologies for probing small RNA populations, in part as a member of the ENCODE consortium (with Tom Gingeras, CSHL). Finally, we develop (with Dick McCombie) and apply focal re-sequencing methods for identifying disease relevant mutations, for probing the epigenetic landscape and for the study of human evolution. | rnai, rna, mammal, genetics, genomics, microrna, sirna, pirna, gene regulation, cancer biology, stem cell biology, defense, genome, transposon, cancer, stem cell | has parent organization: Cold Spring Harbor Laboratory | nlx_151354 | SCR_005982 | Cold Spring Harbor Laboratory - Hannon Lab | 2026-02-11 10:57:17 | 66 |
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