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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Yeast Search for Transcriptional Regulators And Consensus Tracking Resource Report Resource Website 100+ mentions |
Yeast Search for Transcriptional Regulators And Consensus Tracking (RRID:SCR_006076) | YEASTRACT | database, data or information resource | A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database. | yeast, gene, regulatory association, transcription factor, target gene, genomic, transcription regulation, transcription, web service, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SGD is related to: Gene Ontology is related to: Regulatory Sequence Analysis Tools |
Fundacao para a Ciencia e a Tecnologia contract Pest-OE/EQB/LA0023/2011_research line: Systems and Synthetic Biology; Fundacao para a Ciencia e a Tecnologia ERA-IB/0002/2010; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-EIA/111239/2009; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-CCO/118522/2010 |
PMID:24170807 PMID:20972212 PMID:18032429 PMID:16381908 |
Free | nif-0000-03652, OMICS_00547, biotools:yeastract | https://bio.tools/yeastract | SCR_006076 | 2026-08-08 12:04:06 | 130 | |||||
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VirHostNet: Virus-Host Network Resource Report Resource Website 1+ mentions |
VirHostNet: Virus-Host Network (RRID:SCR_005978) | VirHostNet | database, data or information resource | Public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. It contains high quality and up-to-date information gathered and curated from public databases (VirusMint, Intact, HIV-1 database). It allows users to search by host gene, host/viral protein, gene ontology function, KEGG pathway, Interpro domain, and publication information. It also allows users to browse viral taxonomy. | interaction, protein, virus, protein-protein interaction, protein interaction, infectious disease, antiviral drug design, proteome, interactome, molecular function, cellular pathway, protein domain, virus-virus, virus-host, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: VirusMINT is related to: IntAct is related to: HIV-1 Human Protein Interaction Database is related to: PSICQUIC Registry has parent organization: Claude Bernard University Lyon 1; Lyon; France |
PMID:18984613 | Acknowledgement requested, Public | nif-0000-03634, OMICS_01910, biotools:virhostnet | https://bio.tools/virhostnet | SCR_005978 | Virus-Host Network | 2026-08-08 12:04:01 | 7 | |||||
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ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | 2026-08-08 12:03:58 | 3 | ||||||
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targetHub Resource Report Resource Website 1+ mentions |
targetHub (RRID:SCR_006522) | targetHub | database, data or information resource | A database of miRNA-mRNA interactions. The interaction data is obtained from various external data sources and in some cases computed in-house by algorithms implemented for miRNA target prediction. |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
OMICS_00418 | SCR_006522 | 2026-08-08 12:03:58 | 4 | ||||||||||
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SILVA Resource Report Resource Website 10000+ mentions |
SILVA (RRID:SCR_006423) | database, data or information resource | High quality ribosomal RNA databases providing comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Supplementary services include a rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. Alignment tool, SINA, is available for download as well as available for use online. | ribosomal rna, gene sequence, gene, sequence, alignment, taxonomy, 16s, 18s, 23s, 28s, phylogeny, probe, primer, alignment service, fish, arb, ribocon, geoblast, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: RNAcentral is related to: ARB project is related to: SINA is related to: European ribosomal RNA database has parent organization: German Collection of Microorganisms and Cell Cultures |
German Collection of Microorganisms and Cell Cultures | PMID:23193283 PMID:24293649 PMID:17947321 |
biotools:silva, OMICS_01514, nif-0000-03464, r3d100011323, rid_000103 | https://bio.tools/silva, https://doi.org/10.17616/R3FP60 | SCR_006423 | SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-08-08 12:04:08 | 15971 | ||||||
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DBM-DB Resource Report Resource Website 10+ mentions |
DBM-DB (RRID:SCR_006258) | DBM-DB | database, data or information resource | Database storing and integrating genomic data of diamondback moth (DBM), Plutella xylostella (L.). It provides comprehensive search tools and downloadable datasets for scientists to study comparative genomics, biological interpretation and gene annotation of this insect pest. DBM-DB contains assembled transcriptome datasets from multiple DBM strains and developmental stages, and the annotated genome of P. xylostella (version 2). They have also integrated publically available ESTs from NCBI and a putative gene set from a second DBM genome (KONAGbase) to enable users to compare different gene models. DBM-DB was developed with the capacity to incorporate future data resources, and will serve as a long-term and open-access database that can be conveniently used for research on the biology, distribution and evolution of DBM. This resource aims to help reduce the impact DBM has on agriculture using genomic and molecular tools. | genome, rna-seq, gene expression profiling, micrornas, metagenomics, blast, gbrowse, FASEB list |
is listed by: OMICtools has parent organization: Fujian Agriculture and Forestry University; Fujian; China |
PMID:24434032 | Free, Public | OMICS_02235 | http://59.79.254.1/DBM/ | SCR_006258 | Diamondback moth Genome Database | 2026-08-08 12:04:03 | 32 | |||||
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CMGRN Resource Report Resource Website |
CMGRN (RRID:SCR_006412) | CMGRN | analysis service resource, data analysis service, production service resource, service resource | A web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data. | chip-seq, gene expression, gene regulatory network |
is listed by: OMICtools has parent organization: Hong Kong Baptist University; Hong Kong; China |
PMID:24389658 | OMICS_02199 | http://bioinfo.icts.hkbu.edu.hk/cmgrn | SCR_006412 | Constructing Multi-level Gene Regulatory Networks, CMGRN - constructing multi-level gene regulatory networks using ChIP-seq and gene expression data | 2026-08-08 12:04:04 | 0 | ||||||
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GeneReviews Resource Report Resource Website 100+ mentions |
GeneReviews (RRID:SCR_006560) | GeneReviews | database, data or information resource | Provides clinically relevant and medically actionable information for inherited conditions in standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families. Searchable book of expert-authored, peer-reviewed disease descriptions presented in standardized format and focused on clinically relevant and medically actionable information on diagnosis, management, and genetic counseling of patients and families with specific inherited conditions. | genetics, disease, clinical, diagnosis, management, genetic counseling, gene, chromosomal locus, phenotype, allele, locus, mutation |
is used by: NIF Data Federation is listed by: OMICtools has parent organization: NCBI has parent organization: University of Washington; Seattle; USA |
Inherited disease | PMID:20301295 | Acknowledgement required, Protected by copyright | OMICS_00269 | SCR_006560 | 2026-08-08 12:04:09 | 127 | ||||||
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DECIPHER Resource Report Resource Website 1000+ mentions |
DECIPHER (RRID:SCR_006552) | DECIPHER | database, data or information resource | Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes. | chromosomal imbalance, phenotype, chromosome, gene, genome, deletion, duplication, copy number, genotype, polymorphism, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Deciphering Developmental Disorders is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Microdeletion Syndrome, Overgrowth syndrome, Microduplication syndrome, Deletion syndrome, Duplication syndrome, Wolf-Hirschhorn Syndrome, Williams-Beuren Syndrome, Smith-Magenis Syndrome, Etc | Wellcome Trust WT077008 | PMID:19344873 | Acknowledgement required | nlx_151653, OMICS_00265 | SCR_006552 | Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources, Decipher | 2026-08-08 12:04:04 | 1991 | ||||
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DroID - Drosophila Interactions Database Resource Report Resource Website 10+ mentions |
DroID - Drosophila Interactions Database (RRID:SCR_006634) | DroID | database, data or information resource | A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available. | interaction, gene, protein, protein interaction, annotation, transcription factor, rna, protein-protein interaction, interactome, gene expression, phenotype, interolog, ortholog |
is listed by: OMICtools is related to: Cytoscape has parent organization: Wayne State University School of Medicine; Michigan; USA |
PMID:21036869 PMID:18840285 |
Free, Public, Acknowledgement requested | nif-0000-02767, OMICS_01908 | SCR_006634 | DroID - The Drosophila Interactions Database | 2026-08-08 12:04:05 | 37 | ||||||
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waviCGH Resource Report Resource Website 1+ mentions |
waviCGH (RRID:SCR_006662) | waviCGH | analysis service resource, data analysis service, production service resource, service resource | A versatile web-server application for the analysis and visualization of array-CGH data. | genomic, copy number alteration, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20507915 | Acknowledgement requested | OMICS_00739, biotools:wavicgh | https://bio.tools/wavicgh | SCR_006662 | 2026-08-08 12:03:59 | 4 | ||||||
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Database of Arabidopsis Transcription Factors Resource Report Resource Website 10+ mentions |
Database of Arabidopsis Transcription Factors (RRID:SCR_007101) | DATF | database, data or information resource | Database that collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families. It uses not only locus (gene), but also gene model (transcript, protein) and the detail information is for each gene model not for locus. It adds multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Rice Transcription Factors (DRTF). It also keeps old information items such as the unique cloned and sequenced information of about 1200 transcription factors, protein domains, 3D structure information with BLAST hits against PDB, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference. | gene, alignment, arabidopsis, binding, clone, dna, domain, locus, phylogenetic tree, transcription, chromosome, transcription factor, blast, family, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
State Key Laboratory of Protein and Plant Gene Research ; National Natural Science Foundation of China 31470330; China 863 Programs 2006AA02Z334; China Postdoctoral Science Foundation Grant 2014M560017 |
PMID:15731212 | Free | nif-0000-21112, OMICS_00551, biotools:datf | https://bio.tools/datf | SCR_007101 | 2026-08-08 12:04:11 | 37 | |||||
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Therapeutic Target Database Resource Report Resource Website 50+ mentions |
Therapeutic Target Database (RRID:SCR_006892) | TTD | database, data or information resource | A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs/ligands directed at each of these targets. Also included in this database are links to relevant databases that contain information about the function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and related literatures of each target.This database currently contains 1535 targets and 2107 drugs/ligands. Queries can be submitted by entering or selecting the required information in any one or combination of the five fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. | therapeutic, protein, nucleic acid, disease, pathway, drug, ligand, target, FASEB list |
is listed by: OMICtools is related to: ConsensusPathDB has parent organization: National University of Singapore; Singapore; Singapore |
nif-0000-03596, OMICS_01593 | http://bidd.nus.edu.sg/group/cjttd/ | SCR_006892 | 2026-08-08 12:04:10 | 73 | ||||||||
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Kinetic Data of Bio-molecular Interaction Resource Report Resource Website |
Kinetic Data of Bio-molecular Interaction (RRID:SCR_007064) | KDBI | database, data or information resource | A collection of experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligandbinding or reaction events described in the literature. Currently, KDBI contains 63 pathway simulation parameter sets, 19,263 records (about 2.3 fold of 8,273 in year 2003) of 10,532 distinctive bio-molecular binding and 11,954 interaction events, which involve 2,635 proteins/protein complexes, 847 nucleic acids, 1603 small molecules and more than 100 pathways. | kinetic, protein-protein, protein-rna, protein-dna, protein-ligand, rna-ligand, dna-ligandbinding, reaction event, biomolecule, interaction |
is listed by: OMICtools has parent organization: National University of Singapore; Singapore; Singapore |
PMID:18971255 | Non-commercial | nif-0000-03066, OMICS_00539 | SCR_007064 | 2026-08-08 12:04:11 | 0 | |||||||
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Database of Genomic Variants Resource Report Resource Website 100+ mentions |
Database of Genomic Variants (RRID:SCR_007000) | DGV | database, data or information resource | Collection of curated structural variation in the human genome. Catalogue of human genomic structural variation identified in healthy control samples for studies aiming to correlate genomic variation with phenotypic data. It is continuously updated with new data from peer reviewed research studies. The Database is no longer accepting direct submission of data as they are currently part of a collaboration with two new archival CNV databases at EBI and NCBI, called DGVa and dbVAR, respectively. One of the changes to DGV as part of this collaborative effort is that they will no longer be accepting direct submissions, but rather obtain the datasets from DGVa (short for DGV archive). This will ensure that the three databases are synchronized, and will allow for an official accessioning of variants. | genome, chromosome, control, deletion, structure, insertion, inversion, segmental duplication, structural variation, genomic variation, phenotype, copy number variation, indel, genetics, gene expression, chromosome abnormality, human genome, variation, dna, statistics, chromosome, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Database of Genomic Variants Archive (DGVa) is related to: dbVar |
Healthy, Control | Genome Canada ; Ontario Genomics Institute ; McLaughlin Centre ; Canadian Institutes of Health Research |
PMID:24174537 | Acknowledgement requested | nif-0000-02721, OMICS_00266, r3d100010346 | http://projects.tcag.ca/variation/, https://doi.org/10.17616/R3NC8H | SCR_007000 | DGV, Database of Genomic Variants | 2026-08-08 12:04:01 | 419 | |||
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Public Expression Profiling Resource Resource Report Resource Website 10+ mentions |
Public Expression Profiling Resource (RRID:SCR_007274) | PEPR | database, data or information resource | An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ). | microarray, expression profiling, affymetrix, metadata standard, gene, time series, data sharing, visualization, data mining, platform, blood, cell, cancer, bone, brain, eye, gut, heart, kidney, liver, lung, muscle, spinal cord, spleen, analysis |
is listed by: OMICtools is related to: Gene Expression Omnibus |
NINDS ; United States Department of Defense ; NHGRI ; NHLBI |
PMID:14681485 PMID:14596642 |
Public, Account required, (to download, For the analysis and visualization tools), The community can contribute to this resource | nif-0000-00014, OMICS_00776 | SCR_007274 | 2026-08-08 12:04:12 | 16 | ||||||
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EpiExplorer Resource Report Resource Website 10+ mentions |
EpiExplorer (RRID:SCR_007301) | EpiExplorer | analysis service resource, data analysis service, production service resource, service resource | A web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborious preprocessing. | is listed by: OMICtools | PMID:23034089 | Acknowledgement requested | OMICS_00632 | SCR_007301 | 2026-08-08 12:04:12 | 29 | ||||||||
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Yeast Intron Database Resource Report Resource Website 1+ mentions |
Yeast Intron Database (RRID:SCR_007144) | Yeast Intron Database | database, data or information resource | Database of information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Listed are known spliceosomal introns in the yeast genome and the splice sites actually used are documented. Through the use of microarrays designed to monitor splicing, they are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. In version 3.0, expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors is included. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis. | intron, spliceosomal, splicing, genome, intron splice signal, sequence, splice site |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
W. M. Keck Foundation ; Packard Foundation ; NIH |
PMID:11988574 | The community can contribute to this resource | nif-0000-03649, OMICS_01890 | http://www.cse.ucsc.edu/research/compbio/yeast_introns.html | SCR_007144 | Ares lab Yeast Intron Database | 2026-08-08 12:04:11 | 2 | ||||
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Kevin's GATTACA World Resource Report Resource Website |
Kevin's GATTACA World (RRID:SCR_007191) | data or information resource, blog, narrative resource | A Weblog on Bioinformatics, Genome Science and Next Generation Sequencing. | is listed by: OMICtools | OMICS_01716 | SCR_007191 | Kevins GATTACA World | 2026-08-08 12:04:02 | 0 | ||||||||||
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CistromeFinder Resource Report Resource Website 1+ mentions |
CistromeFinder (RRID:SCR_005405) | CistromeFinder | data or information resource, data set | Data portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations (May 2013). Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update. | chip-seq, dnase-seq, cell, tissue, disease, histone modification, transcription factor, chromatin regulator, dnase, binding site, gene, transcription regulation |
is listed by: OMICtools is related to: UCSC Genome Browser is related to: CistromeMap has parent organization: Dana-Farber Cancer Institute |
PMID:23508969 | The community can contribute to this resource | OMICS_00528 | SCR_005405 | 2026-08-08 12:05:51 | 2 |
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