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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Public Expression Profiling ResourceResource, data or information resource, databaseAn 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, analysisSCR_007274(Public Expression Profiling Resource, RRID:SCR_007274)NHGRI, NHLBI, NINDS, United States Department of Defenserelated to: Gene Expression Omnibus, listed by: OMICtoolsReferences (2)Last checked downnif-0000-00014, OMICS_00776
Hereditary Hearing Loss HomepageResource, atlas, topical portal, database, portal, data or information resourceOverview of the genetics of hereditary hearing impairment for researchers and clinicians. The site lists data and references for all known gene localizations and identifications for nonsyndromic hearing impairment, and several for syndromic hearing loss. For syndromic hearing impairment, only a few of the most frequent forms are covered. An atlas of cochlea with genes listed can be accessed from this site.cochlea, syndromic, nonsyndromic, gene, genetics, hearing impairment, hearing, earSCR_006469(Hereditary Hearing Loss Homepage, RRID:SCR_006469) University of Antwerp; Antwerp; Belgium , University of Iowa; Iowa; USA Hereditary hearing impairment, Hearing impairmentrelated to: MITOMAP - A human mitochondrial genome database, listed by: OMICtoolsLast checked upnif-0000-00075, OMICS_01542
WormAtlasResource, atlas, narrative resource, database, training material, data or information resourceAnatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. \\nIncludes links to other major worm websites and databases.electron, ganglion, anatomy, caenorhabditis elegan, c. elegan, cell, development, gfpworm, glossary, lineage, microscopy, morphology, video, nematode, nerve cord, nervous system, neuroanatomy, neuron, phenotype, wiring diagram, worm, imageSCR_007295(WormAtlas, RRID:SCR_007295)Albert Einstein College of Medicine; New York; USA NCRR, NIH Division of Research Resources, NIH Office of the Directorrelated to: Expression Patterns for C. elegans promoter GFP fusions, listed by: OMICtoolsLast checked upnif-0000-00098https://orip.nih.gov/comparative-medicine/programs/invertebrate-models
RNA Abundance Database Resource, resource, database, service resource, storage service resource, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, Documented on March 24, 2014. A resource for gene expression studies, storing highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data were available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) were available from this website. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. NOTE: Due to changes in technology and funding, the RAD website is no longer available. RAD as a schema is still very much active and incorporated in the GUS (Genomics Unified Schema) database system used by CBIL (EuPathDB, Beta Cell Genomics) and others. The schema for RAD can be viewed along with the other GUS namespaces through our Schema Browser.gene expression, gene, affymetrix, biomaterial, genomics, microarray, mpss, ontology, rna, rt-pcr, sage, functional genomics, transcript abundanceSCR_002771( RNA Abundance Database , RRID:SCR_002771)University of Pennsylvania; Philadelphia; Pennsylvania NHGRI, NIDDK, NIHrelated to: MIAME, MGED Ontology, MicroArray and Gene Expression Markup Language, listed by: OMICtoolsLast checked upnif-0000-00133, OMICS_00869
NeuroMabResource, reagent supplier, material resource, antibody supplierA national mouse monoclonal antibody generating resource for biochemical and immunohistochemical applications in mammalian brain. NeuroMabs are generated from mice immunized with synthetic and recombinant immunogens corresponding to components of the neuronal proteome as predicted from genomic and other large-scale cloning efforts. Comprehensive biochemical and immunohistochemical analyses of human, primate and non-primate mammalian brain are incorporated into the initial NeuroMab screening procedure. This yields a subset of mouse mAbs that are optimized for use in brain (i.e. NeuroMabs): for immunocytochemical-based imaging studies of protein localization in adult, developing and pathological brain samples, for biochemical analyses of subunit composition and post-translational modifications of native brain proteins, and for proteomic analyses of native brain protein networks. The NeuroMab facility was initially funded with a five-year U24 cooperative grant from NINDS and NIMH. The initial goal of the facility for this funding period is to generate a library of novel NeuroMabs against neuronal proteins, initially focusing on membrane proteins (receptors/channels/transporters), synaptic proteins, other neuronal signaling molecules, and proteins with established links to disease states. The scope of the facility was expanded with supplements from the NIH Blueprint for Neuroscience Research to include neurodevelopmental targets, the NIH Roadmap for Medical Research to include epigenetics targets, and NIH Office of Rare Diseases Research to include rare disease targets. These NeuroMabs will then be produced on a large scale and made available to the neuroscience research community on an inexpensive basis as tissue culture supernatants or purified immunoglobulin by Antibodies Inc. The UC Davis/NIH NeuroMab Facility makes NeuroMabs available directly to end users and is unable to accommodate sales to distributors for third party distribution. Note, NeuroMab antibodies are now offered through antibodiesinc.antibody, brain, channel, disease-related protein, k channel subunit, mab, mammalian, membrane protein, monoclonal antibody, mouse, neuronal monoclonal antibody, neuronal protein, neuronal signaling molecule, reagent, receptor, research reagent, synaptic protein, transporterSCR_003086(NeuroMab, RRID:SCR_003086)University of California at Davis; California; USA Antibodies Inc., NIH Blueprint for Neuroscience Research, NIH Roadmap for Medical Research, NIMH, NINDS, Office of Rare Diseases Researchused by: NIF Data Federation, listed by: OMICtoolsLast checked upnif-0000-00175, OMICS_01774http://www.neuromab.org
Information Hyperlinked Over ProteinsResource, service resource, data or information resource, databaseInformation system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-miningSCR_004829(Information Hyperlinked Over Proteins, RRID:SCR_004829)Autonomous University of Madrid; Madrid; Spain European Unionrelated to: PubMed, listed by: OMICtoolsPMID:15226743Last checked upnif-0000-00232, OMICS_01185
PharmGKBResource, data access protocol, database, web service, data set, service resource, storage service resource, software resource, data repository, data or information resourceDatabase and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.pharmacogenomics, microarray, pathway, phenotype, snp array, genotype, clinical, genetic variation, drug, gene, genetic variation, disease, cardiovascular, pulmonary, cancer, metabolic, transporter, drug response, small molecule, research, drug responseSCR_002689(PharmGKB, RRID:SCR_002689)Stanford University; Stanford; California NIGMSrelated to: WikiPathways, ConsensusPathDB, Monarch Initiative, Integrated Molecular Interaction Database, MalaCards, phenomeNET, used by: NIF Data Federation, listed by: OMICtoolsPMID:11908751Last checked upnif-0000-00414, OMICS_01586
SuperTargetResource, data or information resource, databaseDatabase for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range.drug metabolism, drug, cytochrome p450, ontology, pathway, target, compound, cytochrome, drug target, protein, side effect, protein-protein interactionSCR_002696(SuperTarget, RRID:SCR_002696)Charite - Universitatsmedizin Berlin; Berlin; Germany BMBF, DFG, European Union SynSys, NIGMSlisted by: OMICtoolsReferences (2)Last checked downnif-0000-00416, OMICS_01591http://bioinf-tomcat.charite.de/supertarget/, http://bioinformatics.charite.de/supertarget
IMEx - The International Molecular Exchange ConsortiumResource, organization portal, database, consortium, service resource, portal, storage service resource, data repository, community building portal, data or information resourceInteraction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data.protein-protein interaction, nonredundant, protein interaction, interaction, proteomics, metadata standard, short course, molecular interactionSCR_002805(IMEx - The International Molecular Exchange Consortium, RRID:SCR_002805)European Bioinformatics Institute European Unionrelated to: MatrixDB, MPIDB, Database of Interacting Proteins, Database of Interacting Proteins, InnateDB, IntAct, Interaction Reference Index, MPIDB, Universal Protein Resource, InnateDB, MatrixDB, BioGRID, I2D, Molecular Connections NetPro, SIB Swiss Institute of Bioinformatics, IntAct, PSI-MI, PSICQUIC, mentha, Bioconductor, listed by: OMICtools, affiliated with: MINT, works_with: CellPhoneDB, Cytoscape, IntAct, MINT, MPact: Representation of Interaction Data at MIPS, Molecular Connections NetPro, BioGRID, InnateDB, BINDReferences (2)Last checked upnif-0000-00447, OMICS_01545http://imex.sourceforge.net/
MITOMAP - A human mitochondrial genome databaseResource, data or information resource, databaseDatabase of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletionSCR_002996(MITOMAP - A human mitochondrial genome database, RRID:SCR_002996)Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA , Emory University School of Medicine; Georgia; USA Ciber Enfermedades raras, Diputacion General de Aragon Grupos consolidados B33, Ellison Foundation, Muscular Dystrophy Foundation, NHLBI, NIA, NIGMS, NIH, NIH Biomedical Informatics Training Grant, NINDS, NSF, Spanish Fondo de Investigacion Sanitariarelated to: Hereditary Hearing Loss Homepage, used by: HmtVar, listed by: OMICtoolsReferences (5)Last checked upnif-0000-00511, OMICS_01641
Gene WeaverResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resourceFreely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualizationSCR_003009(Gene Weaver, RRID:SCR_003009)Jackson Laboratory Integrative Neuroscience Initiative on Alcoholism, NIAAArelated to: Integrated Manually Extracted Annotation, used by: NIF Data Federation, Integrated Datasets, listed by: OMICtoolsReferences (2)Last checked upnif-0000-00517, OMICS_02232http://ontologicaldiscovery.org/
HUPO Proteomics Standards InitiativeResource, data or information resource, training resource, standard specification, narrative resource, meeting resource, knowledge environment, ontology, controlled vocabularyInitiative to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The main organizational unit is the work group, with a Gel Electrophoresis (GEL) work group, a Mass Spectrometry (MS) work group, a Molecular Interactions (MI) work group, a Protein Modifications (MOD) work group, a Proteomics Informatics (PI) work group, and a Sample Processing (SP) work group. The Gel Electrophoresis (GEL) work group aims to develop reporting requirements that supplement the Minimum Information About a Proteomics Experiment (MIAPE) parent document, describing the minimum information that should be reported about gel-based experimental techniques used in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about gel electrophoresis and informatics performed on gel images. The Mass Spectrometry Standards Working Group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the field of proteomics mass spectrometry. A past achievement is the mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released but is now deprecated in favor of mzML. The Molecular Interactions workgroup is concentrating on improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases; and improving the accessibility of molecular interaction data to the user community. By using a common standard data can be downloaded from multiple sources and easily combined using a single parser. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml. A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the consensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available. These short names are included in the ontology as synonyms of the corresponding terms. The Proteomics Informatics Standards Group (PSI-PI) goals are to provide a set of minimal reporting requirements which augment the MIAPE reporting guidelines with respect to analysis of data derived from proteomics experiments; to provide vendor-neutral and standard formats for representing results of analyzing and processing experimental data; to foster adoption of the format by highlighting efforts made by vendors and individuals that utilize the format in their products. The remit of the Sample Processing Working Group is to produce reporting guidelines, data exchange formats and controlled vocabulary covering all separation techniques not considered to be "classical" one- or two-dimensional gel electrophoresis (cf. the Gel WG home page), along with other kinds of sample handling and processing (for example, "tagging" proteins or peptides, splitting, combining and storing samples). Where possible we seek to develop our products in collaboration with all proteomics stakeholders and, where relevant, developers from other standards communities, most notably metabolomics. * Minimum reporting requirements: The evolving Minimum Information About a Proteomics Experiment (MIAPE) documents offer guidelines on how to adequately report a proteomics experiment. It is expected that these documents will be published, and that the requirements within will be enforced by journals, compliant repositories and funders (cf. MIAME). * XML formats for data exchange: Derived from the FuGE general object model, the formats developed by this workgroup are designed to function both as standalone files and as part of a "parent" FuGE-ML document. These formats will facilitate data exchange between researchers, and submission to repositories or journals. * Controlled vocabularies (CVs) and ontology: Lists of clearly defined terms are crucial for the construction of unambiguously worded data files. In addition to providing supporting CVs for the individual data capture formats as part of the integrated PSI CV, the Sample Processing WG will contribute terms to the Functional Genomics Ontology (FuGO).proteomics, work group, gel electrophoresis, mass spectrometry, molecular interaction, protein modification, proteomics informatics, sample processing, controlled vocabulary, miape, transcriptome, metabolome, proteome, metadata, mass spectrometry informatics, community standards, annotation system, protein-protein interaction, protein, data format, annotation, minimal reporting requirement, nomenclature, reporting guideline, data exchange format, ontology development, rdf developmentSCR_003158(HUPO Proteomics Standards Initiative, RRID:SCR_003158)HUPO - Human Proteome Organisation related to: PRIDE, listed by: OMICtoolsLast checked upnif-0000-00568, OMICS_01781
ProLinks Database of Functional LinkagesResource, software resource, software toolkitTHIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage.functional linkage, protein linkage, inference methodSCR_003185(ProLinks Database of Functional Linkages, RRID:SCR_003185)University of California at Los Angeles; California; USA listed by: OMICtoolsLast checked downnif-0000-00580http://prl.mbi.ucla.edu/prlbeta/prolinks.jsp http://dip.mbi.ucla.edu/dipbeta/prolinks.jsp
PathGuide: the pathway resource listResource, catalog, data or information resource, databaseCatalog containing information about 547 biological pathway related resources and molecular interaction related resources. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.gene interaction network, metabolic pathway, signaling pathway, pathway diagram, protein-compound interaction, protein-protein interaction, protein sequence focused, transcription factor, gene regulatory network, transcription factor target, genetic interaction, pathway, molecular interactionSCR_003248(PathGuide: the pathway resource list, RRID:SCR_003248)related to: PSI-MI, bioDBcore, BioPAX Ontology of Biological Pathways, CellML, SBML, listed by: OMICtoolsPMID:16381921Last checked upnif-0000-00640, OMICS_01701, SciRes_000148
A Classification of Mobile genetic ElementsResource, data or information resource, databaseA database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME.mobile genetic element, phage genome, plasmid, virus, prophage, transposon, protein, gene, classification, data analysis service, prophage predictionSCR_001694(A Classification of Mobile genetic Elements, RRID:SCR_001694)Free University of Brussels; Brussels; Belgium ESTEClisted by: OMICtoolsReferences (2)Last checked upnif-0000-02533, OMICS_01528
AffinDBResource, data or information resource, databaseDatabase of affinity data for protein-ligand complexes of the Protein Data Bank (PDB) providing direct and free access to the experimental affinity of a given complex structure. Affinity data are exclusively obtained from the scientific literature. As of Thursday, May 01st, 2014, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex. AffinDB provides access to data in three different forms:
# Summary information for PDB entry
# Affinity information window
# Tabular reports
protein-ligand complex, affinitySCR_001690(AffinDB, RRID:SCR_001690)Philipps-University Marburg; Marburg; Germany related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank, listed by: OMICtoolsPMID:16381925Last checked upnif-0000-02536, OMICS_01897http://www.agklebe.de/affinity
Arabidopsis Gene Regulatory Information ServerResource, data or information resource, databaseAn information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB).gene regulatory, gene, arabidopsis thaliana, promoter sequence, target gene, transcription factorSCR_006928(Arabidopsis Gene Regulatory Information Server, RRID:SCR_006928)Ohio State University; Ohio; USA NSFlisted by: OMICtoolsReferences (3)Last checked upnif-0000-02540, OMICS_00548
Arabidopsis thaliana Protein Interactome DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseCentralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotypeSCR_001896(Arabidopsis thaliana Protein Interactome Database, RRID:SCR_001896)Northeast Forest University; Harbin; China National Basic Research Program of China, National High Technology Research and Development Program of China, National Natural Science Foundation of China, Science and Technology Commission of Shanghai Municipalityrelated to: Gene Ontology, listed by: OMICtoolsReferences (2)Last checked upnif-0000-02585, OMICS_01898http://atpid.biosino.org/
Bacteriome.orgResource, data or information resource, databaseDatabase integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong.functional interaction, genetics, genome, protein, protein-protein interaction, protein interaction, function, evolution, structure, gene, phylogenetic profile, chromosome, blast, phylogenetic, complex, networkSCR_001934(Bacteriome.org, RRID:SCR_001934)University of Toronto; Ontario; Canada Canadian Institutes of Health Researchlisted by: OMICtoolsReferences (2)Last checked upnif-0000-02592, OMICS_01899http://128.100.134.188/bacteriome/
BAliBASEResource, data set, source code, software resource, data or information resourceA collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences.
Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets.
benchmark alignment, circular permutation, transmembrane sequence, multiple sequence alignment, benchmark, reference alignment, sequence alignment, sequence, alignmentSCR_001940(BAliBASE, RRID:SCR_001940)University of Strasbourg; Strasbourg; France listed by: OMICtoolsReferences (3)Last checked downnif-0000-02594, OMICS_00971http://www-bio3d-igbmc.u-strasbg.fr/balibase/, http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
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