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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
AnimalTFDB
 
Resource Report
Resource Website
100+ mentions
AnimalTFDB (RRID:SCR_001624) AnimalTFDB data or information resource, database A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. transcription factor, dna-binding domain, transcription co-factor, chromatin remodeling factor, gene structure, functional domain, go annotation, protein interaction, ortholog, paralog, 3d structure, pathway, protein-protein interaction, binding site, target, data set, image collection, 3d spatial image, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: Ensembl
has parent organization: Huazhong University of Science and Technology; Wuhan; China
Huazhong University of Science and Technology; Wuhan; China ;
Fundamental Research Funds for the Central Universities 2010MS045;
National Natural Science Foundation of China 31171271
PMID:22080564 THIS RESOURCE IS NO LONGER IN SERVICE nlx_153892, OMICS_01856, biotools:animal_tfdb https://bio.tools/animal_tfdb SCR_001624 Animal Transcription Factor Database 2026-08-05 10:43:25 289
Human Gene Mutation Database
 
Resource Report
Resource Website
1000+ mentions
Human Gene Mutation Database (RRID:SCR_001621) HGMD data or information resource, database Curated database of known (published) gene lesions responsible for human inherited disease. gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphism, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: BIOBASE Corporation
has parent organization: Cardiff University; Wales; United Kingdom
Inherited disease PMID:22948725
PMID:20368137
PMID:20038494
PMID:19348700
PMID:18428754
PMID:18245393
PMID:12754702
PMID:10612821
PMID:9399854
PMID:9066272
PMID:8882888
Free, Freely available nlx_153887, SCR_001888, biotools:hgmd, nif-0000-10459, OMICS_00281 http://www.hgmd.cf.ac.uk/ac/index.php, https://bio.tools/hgmd, SCR_001621 The Human Gene Mutation Database, The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff 2026-08-05 10:43:25 2462
GTEx eQTL Browser
 
Resource Report
Resource Website
100+ mentions
GTEx eQTL Browser (RRID:SCR_001618) data or information resource, database Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets. genetic variation, high-throughput, phenotype, genotype, molecular, molecule, gene, gene expression, snp, trait, expression, quantitative trait locus, expression quantitative trait locus, genome, probe, sequence, statistics, p-value, rna-seq, array, lymphoblastoid, liver, cerebellum, frontal cortex, temporal cortex, pons, gene regulation, tissue, mrna, data set has parent organization: NCBI NIH Common Fund 268201000029C-4-0-2 Free, Freely available nlx_153884 http://www.gtexportal.org/home/ SCR_001618 NCBI GTEx eQTL Browser, Genotype-Tissue Expression eQTL Browser, GTEx (Genotype-Tissue Expression) eQTL Browser, NCBI GTeX eQTL Browser 2026-08-05 10:43:26 111
WegoLoc
 
Resource Report
Resource Website
1+ mentions
WegoLoc (RRID:SCR_001402) WegoLoc data analysis service, production service resource, service resource, analysis service resource Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information. subcellular localization, protein is listed by: OMICtools
is related to: Gene Ontology
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01636 SCR_001402 weighted gene ontology term based subcellular locallization prediction 2026-08-05 10:43:21 4
MINT
 
Resource Report
Resource Website
1000+ mentions
MINT (RRID:SCR_001523) MINT data or information resource, database A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them. protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, ortholog, FASEB list uses: IntAct
uses: PSI-MI
is listed by: re3data.org
is affiliated with: IMEx - The International Molecular Exchange Consortium
is related to: MPIDB
is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions
is related to: InteroPorc
is related to: Interaction Reference Index
is related to: Pathway Commons
is related to: ConsensusPathDB
is related to: VirusMINT
is related to: PSICQUIC Registry
is related to: Agile Protein Interactomes DataServer
has parent organization: University of Rome Tor Vergata; Rome; Italy
works with: IMEx - The International Molecular Exchange Consortium
European Union ;
ENFIN ;
Interaction Proteome Project ;
IMEx - The International Molecular Exchange Consortium ;
HUPO Proteomics Standards Initiative ;
AIRC Associazione Italiana per la Ricerca sul Cancro
PMID:22096227
PMID:24234451
PMID:19897547
PMID:18592188
PMID:18551417
PMID:18428712
PMID:17135203
PMID:11911893
nlx_152821, r3d100010414 https://doi.org/10.17616/R38S3B SCR_001523 MINT, the Molecular INTeraction database, Molecular Interactions Database, Molecular INTeraction database, MINT - the Molecular INTeraction database 2026-08-05 10:43:23 1109
NeuroPedia
 
Resource Report
Resource Website
10+ mentions
NeuroPedia (RRID:SCR_001551) NeuroPedia data or information resource, database A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species. proteomics, peptide, neuropeptide, mass spectrometry assay, peptide sequence, spectrum, homolog has parent organization: Center for Computational Mass Spectrometry NCRR P41-RR024851;
NIDA 5K01DA23065;
NINDS R01 NS24553;
NIDA R01 DA04271;
NIMH R01 MH077305;
NHLBI P01 HL58120
PMID:21821666 Free, Freely available nlx_152894 SCR_001551 NeuroPedia: Neuropeptide database and spectra library 2026-08-05 10:43:24 12
WikiPathways
 
Resource Report
Resource Website
1000+ mentions
WikiPathways (RRID:SCR_002134) data or information resource, service 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, r3d100013316 SCR_002134 Wiki Pathways 2026-08-05 10:43:34 1696
pSTIING
 
Resource Report
Resource Website
1+ mentions
pSTIING (RRID:SCR_002045) pSTIING data or information resource, database A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis. protein-protein, protein-lipid, protein-small molecule, ligand-receptor interaction, receptor-cell type, transcriptional regulatory module, signal transduction module, inflammation, cell migration, tumorigenesis, protein-protein interaction, transcriptional regulatory network, signalling pathway, interaction, protein interaction, motif, domain, protein, gene is listed by: OMICtools
is related to: Gene Ontology
has parent organization: University College London; London; United Kingdom
Inflammation, Tumor, Cancer PMID:16381926 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01916 SCR_002045 Protein Signalling Transcriptional Interactions and Inflammation Networks Gateway, Protein Signalling Transcriptional Interactions & Inflammation Networks Gateway 2026-08-05 10:43:33 2
Phevor
 
Resource Report
Resource Website
1+ mentions
Phevor (RRID:SCR_002273) Phevor data analysis service, production service resource, service resource, analysis service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles. genome interpretation, variant prioritization, disease gene prioritization, phenotype, gene function, disease, genomic, disease-causing allele, gene, function, allele has parent organization: University of Utah School of Medicine; Utah; USA PMID:24702956 THIS RESOURCE IS NO LONGER IN SERVICE SciRes_000139 SCR_002273 Phenotype Driven Variant Ontological Re-Ranking Tool 2026-08-05 10:43:37 9
AceView
 
Resource Report
Resource Website
100+ mentions
AceView (RRID:SCR_002277) AceView/WormGenes data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions. est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standard has parent organization: NCBI THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21007, r3d100010651 https://doi.org/10.17616/R3260G http://www.ncbi.nih.gov/IEB/Research/Acembly/ SCR_002277 AceView genes, AceView/WormGenes, The AceView Genes 2026-08-05 10:43:37 186
Bgee: dataBase for Gene Expression Evolution
 
Resource Report
Resource Website
50+ mentions
Bgee: dataBase for Gene Expression Evolution (RRID:SCR_002028) Bgee data or information resource, database Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression. gene expression, scrna-seq, rna-seq, affymetrix, in situ hybridization, expressed sequence tag, cross specie, comparison, homology, anatomy, developmental stage, gene expression pattern, development, genome, function, chordate, fish, transcriptiome, embryo, adult, mirna, protein coding, prenatal, immature, post-embryonic development, alimentary system, cardiovascular system, nervous system, renal system, reproductive system, respiratory system, skeletal system, ortholog, ontology, FASEB list is related to: Gene Expression Omnibus
is related to: NCBI Sequence Read Archive (SRA)
is related to: ArrayExpress
is related to: Zebrafish Information Network (ZFIN)
is related to: Xenbase
is related to: Mouse Genome Informatics (MGI)
is related to: Berkeley Drosophila Genome Project
is related to: UniGene
is related to: Zebrafish Anatomical Ontology
is related to: eVOC
is related to: Adult Mouse Anatomy Ontology
is related to: Xenopus Anatomy Ontology
is related to: Drosophila anatomy and development ontologies
is related to: Ensembl
has parent organization: SIB Swiss Institute of Bioinformatics
has parent organization: University of Lausanne; Lausanne; Switzerland
Free, Freely available nif-0000-11819, r3d100014596 https://doi.org/10.17616/R31NJNR8 SCR_002028 Bgee: dataBase Gene Expression Evolution, dataBase Gene Expression Evolution 2026-08-05 10:43:31 54
MADELINE
 
Resource Report
Resource Website
1+ mentions
MADELINE (RRID:SCR_001979) MADELINE software application, service resource, software resource Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. gene, genetic, genomic, c, unix, solaris, freebsd, openbsd, macos, ms-windows, cygwin, linux, pedigree, draw, linkage association, family association is listed by: OMICtools
is listed by: Genetic Analysis Software
has parent organization: University of Michigan; Ann Arbor; USA
PMID:17488757 THIS RESOURCE IS NO LONGER IN SERVICE nlx_154446, OMICS_00210 http://eyegene.ophthy.med.umich.edu/#madeline SCR_001979 Madeline 2026-08-05 10:43:31 5
Primate Orthologous Exon Database
 
Resource Report
Resource Website
1+ mentions
Primate Orthologous Exon Database (RRID:SCR_002065) Primate Orthologous Exon Database data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms. alternative splicing, transcript isoform, ortholog, exon, gene, rna-seq, primate, genome is listed by: OMICtools
has parent organization: University of Chicago; Illinois; USA
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01895 SCR_002065 2026-08-05 10:43:33 1
Internet Brain Volume Database
 
Resource Report
Resource Website
1+ mentions
Internet Brain Volume Database (RRID:SCR_002060) IBVD data or information resource, database A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group. anatomy, volume, dsm-iv, normal, schizophrenia, autistic disorder, bipolar disorder, major depressive disorder, alzheimer's disease, attention deficit-hyperactivity disorder, alcohol dependence, dementia, traumatic brain injury, borderline personality disorder, obsessive-compulsive disorder, asperger syndrome, brain, brain structure, in vivo, ex vivo, male, female, gorilla beringei beringei, pongo pygmaeus, volumetric analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: NIF Data Federation
is related to: Integrated Manually Extracted Annotation
has parent organization: Harvard Medical School; Massachusetts; USA
Normal, Alzheimers disease, Seizure, Complex febrile seizure, Holoprosencephaly, Alcohol dependence, Bipolar Disorder, Traumatic brain injury, Schizophrenia The Human Brain Project ;
NINDS NS034189
PMID:21931990 Free, Available for download, Freely available nif-0000-00033 http://www.nitrc.org/projects/ibvd http://www.cma.mgh.harvard.edu/ibvd/ SCR_002060 2026-08-05 10:43:32 4
ConsensusPathDB
 
Resource Report
Resource Website
500+ mentions
ConsensusPathDB (RRID:SCR_002231) CPDB data or information resource, database An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered. gene regulatory network, pathway, gene regulatory network, molecular interaction, interaction, gene regulation, protein interaction, genetic interaction, biochemical reaction, drug-target interaction, molecule, visualization, gene, protein, complex, metabolite, FASEB list is listed by: OMICtools
is related to: BIND
is related to: BioCarta Pathways
is related to: Biological General Repository for Interaction Datasets (BioGRID)
is related to: CORUM
is related to: Database of Interacting Proteins (DIP)
is related to: DrugBank
is related to: HPRD - Human Protein Reference Database
is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism
is related to: Integrating Network Objects with Hierarchies
is related to: InnateDB
is related to: IntAct
is related to: KEGG
is related to: MINT
is related to: MIPS Mammalian Protein-Protein Interaction Database
is related to: MatrixDB
is related to: NetPath
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: PDZBase
is related to: Pathway Interaction Database
is related to: PIG - Pathogen Interaction Gateway
is related to: PINdb
is related to: PharmGKB
is related to: PhosphoPOINT
is related to: PhosphoSitePlus: Protein Modification Site
is related to: Reactome
is related to: Small Molecule Pathway Database
is related to: SignaLink
is related to: SPIKE
is related to: Therapeutic Target Database
is related to: WikiPathways
has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany
European Union HEALTH-F4-2007-200767 PMID:23143270
PMID:21071422
PMID:20847220
PMID:18940869
Free, Freely available nif-0000-02684, OMICS_01903, r3d100012822 https://doi.org/10.17616/R3HF8Z SCR_002231 ConsensusPathDB, ConsensusPathDB-human 2026-08-05 10:43:35 667
DBASS
 
Resource Report
Resource Website
1+ mentions
DBASS (RRID:SCR_002107) DBASS data or information resource, database A database of new exon boundaries induced by pathogenic mutations in human disease genes. pathogen, mutation, disease gene, database, splice, mutation pattern, nucleotide structure, exon boundary, aberrant 3' splice site, aberrant 5' splice site is listed by: OMICtools
has parent organization: University of Southampton; Southampton; United Kingdom
PMID:20929868
PMID:16963498
PMID:16141195
PMID:17576681
Free, Freely available OMICS_01883 http://www.dbass.org.uk/ SCR_002107 2026-08-05 10:43:33 2
VIRsiRNAdb
 
Resource Report
Resource Website
1+ mentions
VIRsiRNAdb (RRID:SCR_006108) VIRsiRNAdb data or information resource, data repository, storage service resource, database, data analysis service, production service resource, service resource, analysis service resource VIRsiRNAdb is a curated database of experimentally validated viral siRNA / shRNA targeting diverse genes of 42 important human viruses including influenza, SARS and Hepatitis viruses. Submissions are welcome. Currently, the database provides detailed experimental information of 1358 siRNA/shRNA which includes siRNA sequence, virus subtype, target gene, GenBank accession, design algorithm, cell type, test object, test method and efficacy (mostly quantitative efficacies). Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. The database has facilities like search, advance search (using Boolean operators AND, OR) browsing (with data sorting option), internal linking and external linking to other databases (Pubmed, Genbank, ICTV). Additionally useful siRNA analysis tools are also provided e.g. siTarAlign for aligning the siRNA sequence with reference viral genomes or user defined sequences. virsiRNAdb would prove useful for RNAi researchers especially in siRNA based antiviral therapeutics development. virus, sirna, shrna, gene, influenza, sars, hepatitis, sirna sequence, virus subtype, target gene, genbank accession, design algorithm, cell type, efficacy, target genome region, target object, experimental assay, off-target, sirna matching, reference viral sequence, influenza virus, hepatitis b virus, hpv, sars corona virus, viral genome, reference genome, align, sirna sequence, fasta, blast, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Institute of Microbial Technology; Chandigarh; India
Influenza, SARS, Hepatitis, Infectious disease Council of Scientific and Industrial Research; New Delhi; India PMID:22139916 Open unspecified license / Freely available nlx_151610, biotools:virsirnadb https://bio.tools/virsirnadb SCR_006108 VIRsiRNAdb - Database of Viral siRNA / shRNA, Viral siRNA Database, Viral siRNA Database (VIRsiRNAdb) 2026-08-05 10:44:25 4
SNPeffect
 
Resource Report
Resource Website
50+ mentions
SNPeffect (RRID:SCR_005091) SNPeffect data or information resource, database, data analysis service, production service resource, service resource, analysis service resource A database for phenotyping human single nucleotide polymorphisms (SNPs)that primarily focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome. They provide a detailed variant analysis using their tools such as: * TANGO to predict aggregation prone regions * WALTZ to predict amylogenic regions * LIMBO to predict hsp70 chaperone binding sites * FoldX to analyse the effect on structure stability Further, SNPeffect holds per-variant annotations on functional sites, structural features and post-translational modification. The meta-analysis tool enables scientists to carry out a large scale mining of SNPeffect data and visualize the results in a graph. It is now possible to submit custom single protein variants for a detailed phenotypic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. single nucleotide polymorphism, phenotyping, mutation, protein-coding variant, molecule, structure, phenotype, non-synonymous coding snp, allelic variation, gene, protein stability, functional site, protein phosphorylation, glycosylation, subcellular localization, protein turnover, protein aggregation, amyloidosis, chaperone interaction, protein variant, FASEB list is listed by: OMICtools
has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium
PMID:22075996
PMID:18086700
PMID:16809394
PMID:15608254
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00187, nif-0000-03480 http://snpeffect.switchlab.org/ SCR_005091 SNPeffect 4 Phenotyping Human Mutations 2026-08-05 10:44:10 59
hmChIP
 
Resource Report
Resource Website
1+ mentions
hmChIP (RRID:SCR_005407) hmChIP data or information resource, database, data analysis service, production service resource, service resource, analysis service resource A database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains >2000 samples from >500 ChIP-seq and ChIP-chip experiments, representing a total of >170 proteins and >10,000,000 protein-DNA interactions (March 2014). A web server provides an interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell type dependencies, and cross-sample variability of protein-DNA interactions. chromatin immunoprecipitation, chip-seq, chip-chip, protein, protein-dna interaction, binding intensity is listed by: OMICtools
has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA
PMID:21450710 The community can contribute to this resource OMICS_00536 SCR_005407 2026-08-05 10:44:14 5
ChEA
 
Resource Report
Resource Website
100+ mentions
ChEA (RRID:SCR_005403) ChEA data or information resource, software application, database, software resource, data analysis service, production service resource, service resource, analysis service resource Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes. chip, transcription factor, interaction, mrna expression, gene, target gene, command-line, chip-chip, chip-seq is listed by: OMICtools
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
PMID:20709693 OMICS_00526 SCR_005403 ChIP Enrichment Analysis 2026-08-05 10:44:14 256

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