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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: Sep 14, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
EchoBASEResource, data or information resource, databaseA database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium.geneSCR_002430(EchoBASE, RRID:SCR_002430)BBSRC, GlaxoSmithKlinePMID:15608209Last checked downnif-0000-02781
DRC - Database of Ribosomal CrosslinksResource, data or information resource, databaseA database of published cross-link data of the E. coli ribosome. The website provides information on rRNA-rRNA cross-links, rRNA-rProteins cross-links, cross-links between ribosomal proteins, tRNA-ribosome cross-links, growing peptide-ribosome cross-links, factors-ribosome cross-links, and mRNA-ribosome cross-links. All data are presented in tables.e coli, escheria coli, factors-ribosome cross-links, cross-links between ribosomal proteins, growing peptide-ribosome cross-links, mrna-ribosome cross-links, ribosome, rrna-rproteins cross-links, rrna-rrna cross-links, trna-ribosome cross-linksSCR_007628(DRC - Database of Ribosomal Crosslinks, RRID:SCR_007628)listed by: 3DVCLast checked downnif-0000-02766
Smart Dictionary LookupResource, service resource, data or information resource, databaseA system that retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm.gene, proteinSCR_000568(Smart Dictionary Lookup, RRID:SCR_000568)University of Manchester; Manchester; United Kingdom uses: Universal Protein Resource, BioThesaurus, listed by: OMICtoolsLast checked upOMICS_01198
Kyoto Encyclopedia of Genes and Genomes Expression DatabaseResource, service resource, data repository, storage service resourceA repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.encyclopedia, endogenous, environment, enzyme, escherichia coli, exogenous, expression, family, functional, gene, genetic, anabaena, bacillus subtilis, biological system, biology, building block, cell, cellular, chemical, community, complex, genome, genomic, hierarchy, interaction, japanese, mapping, metabolic, metabolic pathway databases, microarray, molecular, molecular wiring, nomenclature, order, organism, ortholog, pathway, process, protein, reaction, research, sequence, specie, substance, synechocystisSCR_001120(Kyoto Encyclopedia of Genes and Genomes Expression Database, RRID:SCR_001120)Kyoto University; Kyoto; Japan listed by: LabWorm, affiliated with: KEGGLast checked upnif-0000-21234
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(, RRID:SCR_001934)University of Toronto; Ontario; Canada Canadian Institutes of Health Researchlisted by: OMICtoolsReferences (2)Last checked upnif-0000-02592, OMICS_01899http://
InteroPorcResource, source code, data analysis service, data analysis software, data processing software, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resourceAutomatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, proteinSCR_002067(InteroPorc, RRID:SCR_002067)CEA; Gif sur Yvette; France European Union, French Atomic Energy Commission, French National Agency of Research, Marie Curie Fellowshiprelated to: Integr8 : Access to complete genomes and proteomes, IntAct, MINT, Database of Interacting Proteins, PSICQUIC RegistryPMID:18508856Last checked upnif-0000-20816
CoryneRegNetResource, data or information resource, databaseReference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. It generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure.gene, regulatory network, transcription factor, interaction, cis-regulatory elementSCR_002255(CoryneRegNet, RRID:SCR_002255)Max-Planck-Institute for Informatics; Saarbrucken; Germany related to: Cytoscape, listed by: OMICtoolsReferences (6)Last checked upnif-0000-02689, OMICS_01858
BioCycResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceA collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site.database, pathway/genome databases, PGDB, genome, metabolic pathway, microbiomeSCR_002298(BioCyc, RRID:SCR_002298)Stanford Research Institute International NIGMSrelated to: Pathway Tools, PathCase Pathways Database System, EcoCyc, MetaCyc, HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism, EcoCyc, Gramene, NCBI BioSystems Database, KOBAS, Tuberculosis Database, Pathway Tools, used by: PathCase Pathways Database System, uses: Pathway Tools, listed by: LabWorm, Human Microbiome Project, lists: Pathway Tools, EcoCyc, MetaCyc, HumanCyc: Encyclopedia of Homo sapiens Genes and MetabolismPMID:16246909Last checked upnif-0000-00369
GenevestigatorResource, data analysis service, commercial organization, database, analysis service resource, production service resource, service resource, data or information resourceA high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similaritySCR_002358(Genevestigator, RRID:SCR_002358)Last checked upnif-0000-21172, nif-0000-21172, OMICS_00763
EcoCycResource, data or information resource, databaseDatabase for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.genome, metabolic pathway, transcription, transporters, escherichia coli, transcriptional regulation, metabolism, pathwaySCR_002433(EcoCyc, RRID:SCR_002433)Stanford Research Institute International NCRR, NIGMSrelated to: MultiFun, BioCyc, BioCyc, AmiGO, NCBI BioSystems Database, Pathway Tools, used by: NIF Data Federation, uses: Pathway Tools, listed by: OMICtools, BioCycReferences (2)Last checked upnif-0000-02783, OMICS_01645
EcoGeneResource, data or information resource, databaseDatabase that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download sciences, genomics, proteomics, gene, gene expression, genetics, protein, protein binding, protein-protein interaction, membrane, rna, dna, structure, function, functional annotation, annotation, blastSCR_002437(EcoGene, RRID:SCR_002437)University of Miami Miller School of Medicine; Florida; USA Lucille P. Markey Foundation, NIGMS, NIHrelated to: RefSeq, Colibri, listed by: re3data.orgReferences (2)Last checked upnif-0000-02784
3D Ribosomal Modification Maps DatabaseResource, data or information resource, databaseDatabase of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome.human, plant, arabidopsis, ribosome, eukaryote, eubacteria, archaea, eukaryaSCR_003097(3D Ribosomal Modification Maps Database, RRID:SCR_003097)University of Massachusetts Amherst; Massachusetts; USA NIGMS, U.S. Public Health Servicerelated to: Yeast snoRNA DatabasePMID:17947322Last checked upnif-0000-00552
RegulonDBResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.transcription, gene regulation, operon, bacteria, evolutionary conservation, regulatory phrase, transcriptional regulation, transcriptional regulatory networkSCR_003499(RegulonDB, RRID:SCR_003499)National Autonomous University of Mexico; Mexico City; Mexico Consejo Nacional de Ciencia y Tecnologia, NIGMS, Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologicalisted by: OMICtools, 3DVCPMID:23203884Last checked upnif-0000-03399, OMICS_01868
N-BrowseResource, software resource, web applicationInteractive graphical browser for biological networks and molecular interaction data. The N-Browse server at NYU currently provides access to a variety of large-scale functional genomic datasets from several species.graphical browser, molecular data interface, functional genomicsSCR_004253(N-Browse, RRID:SCR_004253)New York University; New York; USA Department of the Army, NYSTARPMID:18819079Last checked upnlx_26609
BiblioSpecResource, software resource, data or information resource, databaseBiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra. This suite of software tools is for creating and searching MS/MS peptide spectrum libraries. BiblioSpec is available free of charge for noncommercial use through an interactive web-site at The BiblioSpec package contains the following programs: * BlibBuild creates a library of peptide MS/MS spectra from MS2 files. * BlibFilter removes redundant spectra from a library. * BlibSearch searches a spectrum library for matches to query spectra, reporting the results in an SQT file. In addition to the primary programs, the following auxiliary programs are available: * BlibStats writes summary statistics describing a library. * BlibToMS2 writes a library in MS2 file format. * BlibUpdate adds, deletes, or annotates spectra. * BlibPpMS2 processes spectra (bins peaks, removes noise, normalizes intensity) as done in BlibSearch and prints the resulting spectra to a text file. Several reference libraries are available for download. These libraries are updated regularly and are for use under the Linux operating system. You will find libraries for * Escherichia coli * Saccharomyces cerevisiae * Caenorhabditis elegansSCR_004349(BiblioSpec, RRID:SCR_004349)University of Washington; Seattle; USA Last checked upnlx_36841
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
MicrobesOnlineResource, source code, data analysis service, production service resource, analysis service resource, database, service resource, software resource, data or information resourceMicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at, genome, bacteria, archaea, fungi, prokaryoteSCR_005507(MicrobesOnline, RRID:SCR_005507)Lawrence Berkeley National Laboratory DOEPMID:19906701Last checked upnlx_144607
Tractor dbResource, data or information resource, databaseDatabase of computationally predicted Transcription Factors and binding sites in gamma-proteobacterial genomes. The user may browse a map containing all known E. coli transcription factors and regulatory interactions that connect them, and retrieve information on the conservation of each regulatory interaction across the 30 organisms included in the database. Downloading the information is straightforward, and navigation tabs added to dynamic pages ease navigation between the five interfaces of the database. The original prediction approach, based on the representation of binding sites through statistical models was complemented by a new approach that uses known E. coli regulatory sites as the basis for a pattern matching search of regulatory sites. The use of both approaches together resulted in a more intensive exploration of the sequence space of each regulator's binding site. These data should aid researchers in the design of microarray experiments and the interpretation of their results. They should also facilitate studies of Comparative Genomics of the regulatory networks of this group of organisms.gamma-proteobacterial genome, transcription factor binding site, transcription factor, regulatory network, microarray, comparative genomicis, genomeSCR_005610(Tractor db, RRID:SCR_005610)National Laboratory for Scientific Computing; Rio de Janeiro; Brazil listed by: OMICtoolsPMID:17088283Last checked upnif-0000-03574, OMICS_01863,,
FuncAssociate: The Gene Set FunctionatorResource, analysis service resource, data analysis service, service resource, production service resourceA web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online toolgene, gene ontology, statistical analysis, web serviceSCR_005768(FuncAssociate: The Gene Set Functionator, RRID:SCR_005768)Roth Laboratory Canadian Institute for Advanced Research, NHGRI, NHLBI, NIH, NINDSrelated to: Gene Ontology, listed by: Gene Ontology Tools, OMICtoolsReferences (2)Last checked upnlx_149233, OMICS_02264
BiGG DatabaseResource, data or information resource, databaseA knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.biochemical, genetics, genomics, genome, metabolic network, reconstruction, model, metabolic pathway, gene, protein, reaction, metabolite, metabolic reconstruction, compound, pathwaySCR_005809(BiGG Database, RRID:SCR_005809)University of California at San Diego; California; USA Calit2 summer research scholarship, NIGMS, NIH, Ruth L. Kirschstein National Research Service Award - NIH Bioinformatics Training, University of California at San Diego; California; USAused by: BiGGR, uses: SBML, listed by: 3DVCPMID:20426874Last checked upnlx_149299
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