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on page 1 showing 18 out of 18 results

    ADGO

Cite this (ADGO, RRID:SCR_006343)

URL: http://www.btool.org/ADGO2

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

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Cite this (Arabidopsis thaliana Genome Database, RRID:SCR_001901)

URL: http://www.plantgdb.org/AtGDB/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing.

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    BaCelLo

Cite this (BaCelLo, RRID:SCR_011965)

URL: http://gpcr.biocomp.unibo.it/bacello/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

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Cite this (GeneCodis, RRID:SCR_006943)

URL: http://genecodis.cnb.csic.es/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology.

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Cite this (GeneMANIA, RRID:SCR_005709)

URL: http://genemania.org/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, software resource, data or information resource

Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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Cite this (GeneMerge, RRID:SCR_005744)

URL: http://www.oeb.harvard.edu/faculty/hartl/old_site/lab/publications/GeneMerge.html

Resource Type: Resource, data analysis service, production service resource, analysis service resource, software application, service resource, software resource

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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Cite this (GeneTrail, RRID:SCR_006250)

URL: http://genetrail.bioinf.uni-sb.de/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes.

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Cite this (GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool, RRID:SCR_006848)

URL: http://cbl-gorilla.cs.technion.ac.il/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes.

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Cite this (GreenPhylDB, RRID:SCR_002834)

URL: http://www.greenphyl.org/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.

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Cite this (InParanoid: Eukaryotic Ortholog Groups, RRID:SCR_006801)

URL: http://inparanoid.sbc.su.se/cgi-bin/index.cgi

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded.

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Cite this (InteroPorc, RRID:SCR_002067)

URL: http://biodev.extra.cea.fr/interoporc/

Resource Type: Resource, 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 resource

Automatic 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.

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    LegumeIP

Cite this (LegumeIP, RRID:SCR_008906)

URL: http://plantgrn.noble.org/LegumeIP/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression.

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    mirEX

Cite this (mirEX, RRID:SCR_006060)

URL: http://comgen.pl/mirex/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, atlas, data or information resource

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window.

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Cite this (NLSdb: a database of nuclear localization signals, RRID:SCR_003273)

URL: http://rostlab.org/services/nlsdb/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree

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    PhosPhAt

Cite this (PhosPhAt, RRID:SCR_003332)

URL: http://phosphat.uni-hohenheim.de/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, storage service resource, data repository, data or information resource

Database containing information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given. The PhosPhAt service has a built-in plant specific phosphorylation site predictor trained on the experimental dataset for Serine, threonine and tyrosine phosphorylation (pSer, pThr, pTyr). Protein sequences or Arabidopsis AGI gene identifier can be submitted to the predictor. Users and researchers are encouraged to assist in keeping the database current by submitting either published data or unpublished data (MS/MS data required).

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Cite this (Plant Metabolic Network, RRID:SCR_003778)

URL: http://www.plantcyc.org/

Resource Type: Resource, topical portal, ontology, training resource, database, analysis service resource, production service resource, data analysis service, image collection, service resource, portal, storage service resource, data repository, controlled vocabulary, data or information resource

Broad network of plant metabolic pathway databases with two types of databases: a reference database called PlantCyc and single species/taxon databases, such as AraCyc. Additional external metabolic pathway databases are affiliated with the PMN. These databases remain under the autonomous control of the PMN collaborators who provide them. PMN draws upon the work of many individuals with expertise in annotating genomes, generating metabolic pathway databases, curating biochemical information from the literature, and forming extensive network of collaborations with biological databases and biochemistry researchers. In addition to providing biochemical reaction diagrams, organism-specific metabolic maps, detailed descriptions of enzymes and pathways, and links to other resources, the PMN website houses tutorials to help guide teachers and students as they learn more about the valuable bioinformatic data and analysis tools that are crucial elements of modern biological research. Please help expand the content of the PMN databases, including AraCyc and PlantCyc! Any and all new data submissions related to plant biochemical pathways are welcomed. You can also correct an existing pathway. The PMN has several tools available for analyzing the data presented in PlantCyc and the other species-specific metabolic databases. You may browse the pathway ontology, compound ontology, and enzyme commission ontology. *PlantCyc: a comprehensive plant biochemical pathway database, containing curated information from the literature and computational analyses about the genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism. It provides access to manually curated or reviewed information about shared and unique metabolic pathways present in over 350 plant species. * AraCyc: provides access to manually curated or reviewed information about metabolic pathways for the model plant Arabidopsis thaliana. The pathways may be unique to Arabidopsis or shared with other organisms. Data from gene expression, proteomic, and metabolomic experiments in Arabidopsis can be overlaid on a metabolic pathway map using the OMICS Viewer. * PoplarCyc: provides access to manually curated or reviewed information about metabolic pathways for the model tree Populus trichocarpa and a few other related Populus species and hybrids. The pathways may be unique to poplar or shared with other organisms. Data from gene expression, proteomic, and metabolomic experiments in poplar can be overlaid on a metabolic pathway map using the OMICS Viewer.

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    Reactome

Cite this (Reactome, RRID:SCR_003485)

URL: http://www.reactome.org

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

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    TAIR

Cite this (TAIR, RRID:SCR_004618)

URL: http://www.arabidopsis.org

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resource

Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

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