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on page 1 showing 20 out of 31 results from 1 sources

Cite this (AnalyzeReplication, RRID:SCR_012030)

URL: http://home.uchicago.edu/~jiezhou/replication/

Resource Type: Resource, software resource

Source code providing a cost-effectiveness metric for guiding the design of large-scale RNA-seq differentially expressed (DE) studies.

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Cite this ( Array Information Library Universal Navigator , RRID:SCR_006967)

URL: http://ailun.stanford.edu/

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

Re-annotated gene expression / proteomics data from GEO by relating all probe IDs to Entrez Gene IDs once every three months, enabling you to find data from GEO, and compare them from different platforms and species. Platform Annotations adds the latest annotations to any uploaded probe / gene ID list file. Platform Comparison compares any two platforms to find corresponding probes mapping to the same gene. Cross-species mapping maps platform annotations to other species. Gene Search finds deposited platforms and samples in GEO that contain a list of genes. GPL ID Search finds the GPL ID (GEO platform ID) for your array. You can also download the latest annotations files for all arrays and their comprehensive universal gene identifier table, which relates all types of gene / protein / clone identifiers to Entrez Gene IDs for all species. Note: The database was last updated on 4/30/2011. They have successfully mapped 54932732 individual probes from 385099 GEO samples measuring 3519 GEO platforms across 217 species.

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Cite this (ArrayQuest, RRID:SCR_010935)

URL: http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage

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

A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster.

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Cite this (Bgee: a dataBase for Gene Expression Evolution, RRID:SCR_002028)

URL: http://bgee.org/

Resource Type: Resource, data or information resource, database

Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently RNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species.

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Cite this (ChIPXpress, RRID:SCR_006653)

URL: http://www.bioconductor.org/packages/devel/bioc/html/ChIPXpress.html

Resource Type: Resource, software resource

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

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    Gemma

Cite this (Gemma, RRID:SCR_008007)

URL: http://www.chibi.ubc.ca/Gemma

Resource Type: Resource, data or information resource, database

Database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.

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    GEOquery

Cite this (GEOquery, RRID:SCR_000146)

URL: http://www.bioconductor.org/packages/release/bioc/html/GEOquery.html

Resource Type: Resource, software resource

Software that establishes a bridge between GEO and BioConductor.

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    GSE13168

Cite this (GSE13168, RRID:SCR_003651)

URL: http://ranchobiosciences.com/gse13168/

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

Curated data set from a study that assessed the effects of epidermal growth factor and interleukin 1-beta stimulation, and the modulatory effects of glucocorticoids treatment and protein kinase A inhibition, on the airway smooth muscle transcriptome by microarray analysis. The samples from 4 donors were subjected to different stimulations by Il-1b and EGF (or both) with or without pre-treatment with fluticasone, and data was collected at different timepoints.

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    GSE13732

Cite this (GSE13732, RRID:SCR_003648)

URL: http://ranchobiosciences.com/gse13732/

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

Curated data set from a study that developed biomarkers that may predict development of Clinically Isolated Syndrome (CIS) into a full multiple sclerosis. Expression data was taken from 37 CIS patients and 28 healthy controls at baseline. 34 CIS patients and 10 healthy controls were resampled at a second time point, approximately one year later. Patients were followed clinically for up to two years to determine the TTC (time to conversion to MS).

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    GSE1456

Cite this (GSE1456, RRID:SCR_003642)

URL: http://ranchobiosciences.com/gse1456/

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

Curated series of expression data for 159 tumors from which RNA could be collected in sufficient amounts and quality for analysis from breast cancer patients. Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996.

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    GSE17755

Cite this (GSE17755, RRID:SCR_003650)

URL: http://ranchobiosciences.com/gse17755/

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

Curated data set from a study that contains a gene expression profile of peripheral blood cells (PBMCs) isolated from patients (248 in total) with rheumatoid arthritis (RA)/ systemic lupus erythematosus (SLE)/ polyarticular type juvenile idiopathic arthritis (polyJIA)/ Systemic onset juvenile idiopathic arthritis (sJIA) vs healthy children (HC) and healthy individual (HI).

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    GSE20194

Cite this (GSE20194, RRID:SCR_003645)

URL: http://ranchobiosciences.com/gse20194/

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

Curated data set of gene expression data from 230 stage I-III breast cancers that were generated from fine needle aspiration specimens of newly diagnosed breast cancers before any therapy. The biopsy specimens were collected sequentially during a prospective pharmacogenomic marker discovery study between 2000 and 2008. These specimens represent 70-90% pure neoplastic cells with minimal stromal contamination. In the study, patients received 6 months of preoperative (neoadjuvant) chemotherapy including paclitaxel, 5-fluorouracil, cyclophosphamide and doxorubicin followed by surgical resection of the cancer.

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    GSE24060

Cite this (GSE24060, RRID:SCR_003649)

URL: http://ranchobiosciences.com/gse24060/

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

Curated data set from a gene expression profiling study investigating monozygotic twin pairs with various systemic autoimmune diseases. RNA microarray analyses (Agilent Human 1A(V2) 20K oligo arrays) quantified differential gene expression in blood from 20 monozygotic (MZ) twin pairs, to minimize polymorphic gene effects, discordant for SAID (six with systemic lupus erythematosus (SLE), six rheumatoid arthritis (RA), eight idiopathic inflammatory myopathies (IIM)) and 40 unrelated matched controls.

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    GSE27831

Cite this (GSE27831, RRID:SCR_003646)

URL: http://ranchobiosciences.com/gse27831/

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

Curated data set from gene expression profiles of 29 unique samples from uveal melanoma patients that were measured on Affymetrix microarray. In addition, expression of syntenin-1 was measured by RT-PCR and this data is also available in the study.

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    GSE4271

Cite this (GSE4271, RRID:SCR_003643)

URL: http://ranchobiosciences.com/gse4271/

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

Curated data set from a study that investigated 77 primary high-grade astrocytomas and 23 matched recurrences so that changes in gene expression related to both survival and disease progression can be identified. Samples in the study include WHO grade III and IV astrocytomas with a wide range of survival times.

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    GSE4698

Cite this (GSE4698, RRID:SCR_003644)

URL: http://ranchobiosciences.com/gse4698/

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

Curated data set where gene expression profiling was performed on 60 prospectively collected samples of children with first relapse of acute lymphoblastic leukemia enrolled on the relapse trial ALL-REZ BFM 2002 of the Berlin-Frankfurt-Muenster study group.

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    GSE4922

Cite this (GSE4922, RRID:SCR_003557)

URL: http://ranchobiosciences.com/gse4922/

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

Curated data set of a study that investigated the expression profiles of 347 primary invasive breast tumors on Affymetrix microarrays. Three separate breast cancer cohorts were analyzed: 1) Uppsala (n=249), 2) Stockholm (n=58), 3) Singapore (n=40). The Uppsala and Singapore data can be accessed in GSE4922. The Stockholm cohort data can be accessed at GEO Series GSE1456.

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    GSE8650

Cite this (GSE8650, RRID:SCR_003647)

URL: http://ranchobiosciences.com/gse8650/

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

Curated data set from analyzed gene expression profiles in 19 pediatric patients with SoJIA during the systemic phase of the disease (fever and/or arthritis), 25 SoJIA patients with no systemic symptoms (arthritis only or no symptoms), 39 healthy controls, 94 pediatric patients with acute viral and bacterial infections (available under GSE6269), 38 pediatric patients with Systemic Lupus Erythematosus (SLE), and 6 patients with a second IL-1 mediated disease known as PAPA syndrome.

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Cite this ( GUDMAP Ontology , RRID:SCR_002637)

URL: http://www.gudmap.org/Resources/Ontologies.html

Resource Type: Resource, ontology, resource, data or information resource, controlled vocabulary

A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system.

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Cite this (Integrated Manually Extracted Annotation, RRID:SCR_008876)

URL: https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-2

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

A virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.org

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