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on page 1 showing 20 out of 39 results from 1 sources

Cite this (ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters, RRID:SCR_002276)

URL: http://genome.imim.es/datasets/abs2005/index.html

Resource Type: Resource, data or information resource, database

Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.

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    Ancora

Cite this (Ancora, RRID:SCR_001623)

URL: http://ancora.genereg.net/

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

Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.

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Cite this (Animal QTLdb, RRID:SCR_001748)

URL: http://www.animalgenome.org/cgi-bin/QTLdb/index

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

Database of publicly available trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. Besides the QTL data from species listed, the QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into a public databases before a paper may be accepted for publication. User curator accounts are provided for direct data deposit. By searching or browsing the QTLdb, one can: # Find all QTL on one chromosome
# Find all chromosomes that bear QTL for the same trait
# List all QTL from a particular publication
# Find all markers underlining a QTL
# Find DNA sequences associated with certain markers
# Use LocusLink to further search for candidate genes by comparative maps
# Find experiment details in brief for a given publication
# Find all parameters describing a QTL, as well as test statistics
Users can download the QTLdb data from each species or individual chromosome.

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Cite this (Aves Labs, RRID:SCR_001136)

URL: http://www.aveslab.com/

Resource Type: Resource, biomaterial supply resource, reagent supplier, material resource, antibody supplier

An antibody supplier that specializes in high-affinity custom chicken antibody production, providing clients with chicken IgY and other immunoreagents for biomedical research and antibody manufacturing.

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Cite this (BodyMap-Xs, RRID:SCR_001147)

URL: http://bodymap.genes.nig.ac.jp/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008

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Cite this (Brad Smith Magnetic Resonance Imaging of Embryos, RRID:SCR_006300)

URL: http://www-personal.umich.edu/~brdsmith/Research.html

Resource Type: Resource, data set, video resource, image collection, data or information resource

Data set of image collections and movies including Magnetic Resonance Imaging of Embryos, Human Embryo Imaging, MRI of Cardiovascular Development, and Live Embryo Imaging. Individual MRI slice images, three-dimensional images, animations, stereo-pair animations, animations of organ systems, and photo-micrographs are included.

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Cite this (BrainMaps.org, RRID:SCR_006878)

URL: http://brainmaps.org

Resource Type: Resource, service resource, storage service resource, atlas, image repository, data repository, data or information resource

An interactive multiresolution brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and integrated with a high-speed database for querying and retrieving data about brain structure and function. Currently featured are complete brain atlas datasets for various species, including Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, Tyto alba and many other vertebrates. BrainMaps is currently accepting histochemical, immunocytochemical, and tracer connectivity data, preferably whole-brain. In addition, they are interested in EM, MRI, and DTI data.

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Cite this (Chicken Gene Nomenclature Consortium, RRID:SCR_004966)

URL: http://birdgenenames.org/cgnc/

Resource Type: Resource, database, international standard specification, standard specification, narrative resource, service resource, storage service resource, data repository, data or information resource

International group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated from biocurators and interested contributors. A Human Chicken Ortholog Predictions Search is available. Both resources are part of a united CGNC effort and nomenclature data is shared and co-ordinated between these two resources. They strongly encourage researchers with domain knowledge to participate in this nomenclature effort by requesting a login and providing gene nomenclature for their genes of interest. Please contact them for further information or assistance. The AGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees, including the Chicken Gene Nomenclature Committee (CGNC). The Avian and Chicken nomenclature efforts are co-ordinated and chicken data is shared between these two groups.

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Cite this (Comparative Toxicogenomics Database, RRID:SCR_006530)

URL: http://ctdbase.org/

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

A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.

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    CRCView

Cite this (CRCView, RRID:SCR_007092)

URL: http://crcview.hegroup.org/

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

Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.

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Cite this (Disease Genes Conserved Sequence Tags Database, RRID:SCR_000760)

URL: http://dgcst.ceinge.unina.it/

Resource Type: Resource, data or information resource, database

A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions.

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Cite this (ECgene: Gene Modeling with Alternative Splicing, RRID:SCR_007634)

URL: http://genome.ewha.ac.kr/ECgene/

Resource Type: Resource, data or information resource, database

Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns.

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Cite this (EGAN: Exploratory Gene Association Networks, RRID:SCR_008856)

URL: http://akt.ucsf.edu/EGAN/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible

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Cite this (EID: Exon-Intron Database, RRID:SCR_002469)

URL: http://bpg.utoledo.edu/~afedorov/lab/eid.html

Resource Type: Resource, data set, data or information resource

Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.

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Cite this (Ensembl Variation, RRID:SCR_001630)

URL: http://uswest.ensembl.org/info/docs/variation/index.html

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

Database that stores areas of the genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. There are different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). The effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run the same analysis on your own data using the Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to a quality control process to flag suspect data. In human, they calculate the linkage disequilibrium for each variant, by population.

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Cite this (FuncAssociate: The Gene Set Functionator, RRID:SCR_005768)

URL: http://llama.mshri.on.ca/funcassociate/

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

A 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 tool

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    FunctSNP

Cite this (FunctSNP, RRID:SCR_000393)

URL: http://functsnp.sourceforge.net/

Resource Type: Resource, software resource

An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge.

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Cite this (GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database, RRID:SCR_007440)

URL: http://www.geisha.arizona.edu/geisha/

Resource Type: Resource, database, narrative resource, service resource, storage service resource, atlas, data repository, experimental protocol, data or information resource

Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA.

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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 (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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