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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SitEx Resource Report Resource Website 1+ mentions |
SitEx (RRID:SCR_006122) | SitEx | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms. | projection, protein, functional site, exon, blast, structure, function, gene, amino acid, encoding gene, proteome, ligand, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Ministry of Science and Education 14.740.11.0001; Ministry of Science and Education 07.514.11.4003; Interdisciplinary Integrative Project 35 of SB RAS ; Russian Foundation for Basic Research 11-04-92712; EU-FP7 260429; Program of RAS ; DAAD Leonard Euler Program Grant |
PMID:22139920 | THIS RESOURCE IS NO LONGER IN SERVICE. | biotools:sitex, nlx_151602 | https://bio.tools/sitex | SCR_006122 | SitEx Database | 2026-08-29 11:22:33 | 1 | ||||
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Predictive Networks Resource Report Resource Website |
Predictive Networks (RRID:SCR_006110) | PN | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, source code | A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. | gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: SourceForge |
NLM 1R01LM010129 | PMID:22096235 | Apache License, v2 | nlx_151582, biotools:predictivenetworks | https://bio.tools/predictivenetworks | SCR_006110 | 2026-08-29 11:22:31 | 0 | |||||
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NHMRC Australian PhenomeBank Resource Report Resource Website 1+ mentions |
NHMRC Australian PhenomeBank (RRID:SCR_006149) | APB | biomaterial supply resource, cell repository, material resource, organism supplier | The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. | RIN, Resource Information Network, murine, mutation, gene, strain, transgenic, alteration, phenotype, live mouse, sperm, embryo, transgene, database, allele, chromosome, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network has parent organization: Australian Phenomics Network works with: International Mouse Strain Resource |
Public | nlx_151640 | http://pb.apf.edu.au/phenbank/foreignPageImport.html?page=http://pbstatic.apf.edu.au:80/phenbank/home.htm | SCR_006149 | Australian Phenome Bank, Phenome Bank, Australian PhenomeBank, NHMRC Australian Phenome Bank, PhenomeBank | 2026-08-29 11:22:32 | 3 | ||||||
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Federation of International Mouse Resources Resource Report Resource Website 1+ mentions |
Federation of International Mouse Resources (RRID:SCR_006137) | FIMRe | community building portal, data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7, 2022. Federation of International Mouse Resources (FIMRe) is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. Goals of the Federation of International Mouse Resources: * Coordinate repositories and resource centers to: ** archive valuable genetically defined mice and ES cell lines being created worldwide ** meet research demand for these genetically defined mice and ES cell lines * Establish consistent, highest quality animal health standards in all resource centers * Provide genetic verification and quality control for genetic background and mutations * Provide resource training to enhance user ability to utilize cryopreserved resources | embryo, gamete, embryonic stem cell, embryonic stem cell line, live breeding stock, live mouse, resource center, international network, mouse model, human disease, gene, genome, biomaterial supply resource, cell repository, organism supplier, biospecimen repository, mutation, cryopreserved |
is related to: Jackson Laboratory is related to: Mutant Mouse Resource and Research Center is related to: European Mouse Mutant Archive is related to: RIKEN BioResource Center has parent organization: Mouse Genome Informatics (MGI) |
PMID:16688526 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_151627 | SCR_006137 | Federation of International Mouse Resources (FIMRe) | 2026-08-29 11:22:33 | 4 | ||||||
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SpliceDisease Resource Report Resource Website 1+ mentions |
SpliceDisease (RRID:SCR_006130) | SpliceDisease | data or information resource, data repository, database, service resource, storage service resource | Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser. | rna splicing, mutation, disease, gene, genomic sequence, nucleotide substitution, deletion, insertion, mutation location, splicing mutation, nucleotide, disease association, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 81001481 | PMID:22139928 | The community can contribute to this resource | biotools:splicedisease_db, nlx_151614 | https://bio.tools/splicedisease_db | SCR_006130 | Splice Disease, SpliceDisease Database Site, Splice Disease Database, SpliceDisease Database | 2026-08-29 11:22:32 | 2 | ||||
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Impress Resource Report Resource Website 50+ mentions |
Impress (RRID:SCR_006160) | IMPReSS | data access protocol, data or information resource, experimental protocol, international standard specification, narrative resource, software resource, standard specification, web service | Contains standardized phenotyping protocols essential for the characterization of mouse phenotypes. IMPReSS holds definitions of the phenotyping Pipelines and mandatory and optional Procedures and Parameters carried out and data collected by international mouse clinics following the protocols defined. This allows data to be comparable and shareable and ontological annotations permit interspecies comparison which may help in the identification of phenotypic mouse-models of human diseases. The IMPC (International Mouse Phenotyping Consortium) core pipeline describes the phenotype pipeline that has been agreed by the research institutions. IMPReSS has a SOAP web service machine interface. The WSDL can be accessed here: http://www.mousephenotype.org/impress/soap/server?wsdl | phenotype, phenotyping, adult, embryonic, ontology, enu-induced gene knockout, gene, knockout mouse, ethylnitrosourea |
is related to: European Mouse Phenotyping Resource of Standardised Screens has parent organization: International Mouse Phenotyping Consortium (IMPC) |
nlx_151661 | SCR_006160 | International Mouse Phenotyping Resource of Standardised Screens, IMPReSS - International Mouse Phenotyping Resource of Standardised Screens | 2026-08-29 11:22:33 | 66 | ||||||||
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cafe variome Resource Report Resource Website 10+ mentions |
cafe variome (RRID:SCR_006162) | Cafe Variome | data or information resource, data repository, data set, service resource, storage service resource | Clearinghouse and exchange portal for gene variant (mutation) data produced by diagnostics laboratories, offering users a portal through which to announce, discover and acquire a comprehensive listing of observed neutral and disease-causing gene variants in patients and unaffected individuals. Cafe Variome is not a ''''database'''' for the hosting/display/release of data, but a shop window for finding data. As such, it holds only core info for each record, and uses this merely to enable holistic searching across resources. Diagnostics laboratories routinely assess DNA samples from patients with various inherited disorders, and so produce a great wealth of data on the genetic basis of disease. Unfortunately, those data are not usually shared with others. To address this gross deficiency, a novel system has been developed that aims to facilitate the automated transfer of diagnostic laboratory data to the wider community, via an internet based Cafe for routinely exchanging genetic variation data. The flow of research data concerning the genetic basis of health and disease is critical to understanding and developing treatments for a range of genetic diseases. Overall, the project aims to lower the barriers and provide incentives for a willing community to share data, and thereby facilitate the broader exploitation of diagnostic laboratory data. Cafe Variome aims to address the above data flow problems by: # Minimizing the effort required to publish variant data # Ensuring attribution for data creators working in diagnostic laboratories Key elements of the project strategy are: * Data publication will be automated by endowing standard analysis tools used by laboratories with an online data submission function. Submissions will be received by a central Internet depot, which will serve as a place where published datasets are advertised, and subsequently discovered by diverse 3rd parties. * Each dataset will be unambiguously linked with the data submitter''''s identity, and systems devised to facilitate citation of published variant datasets so they can be cited in the literature. Data creators will thus be credited for their contributions. Data submitters can use Cafe Variome to simply announce or publicize their data to the world. To enable this, only core, non-identifiable data is submitted to the central repository, enabling users to search and discover records of interest in the source repository. The data are not automatically handed on to the user (unless intended by the submitters). Hence, the concept is used to deal with the challenge of maximally sharing data whilst fully respecting ethico-legal considerations. | phenotype, gene variant, mutation, gene, normal, disease | has parent organization: University of Leicester; Leicester; United Kingdom | Diseased, Healthy | European Union FP7/2007-2013- the GEN2PHEN project | Open access, Restricted access and Linked access | nlx_151664 | SCR_006162 | 2026-08-29 11:22:32 | 11 | ||||||
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MIP-DILI Resource Report Resource Website 1+ mentions |
MIP-DILI (RRID:SCR_003870) | MIP-DILI | consortium, data or information resource, organization portal, portal | Consortium that brings together Europe's top industrial and academic experts to develop new tests that will help researchers detect potential liver toxicity issues much earlier in drug development, saving many patients from the trauma of liver failure. The team aims to deepen the understanding of the science behind drug-induced liver injury, and use that knowledge to overcome the many drawbacks of the tests currently used. A major focus will be on a systematic and evidence-based evaluation of both currently available and new laboratory test systems, including cultures of liver cells in one-dimensional and three dimensional configurations. The project will also develop models that take into account the natural differences between patients. This is important because factors such as certain genes, the liver's immune response, and viral infections have all been associated with an increased risk of DILI. The project will seek to address the current lack of human liver cells available to researchers by using induced pluripotent stem cells (iPSCs) generated from patients who are particularly sensitive to DILI. Another strand of the project will develop computer models to unravel the complex, often inter-related mechanisms behind DILI. Finally, the team will assess how accurate the results of laboratory tests are at predicting actual outcomes in patients. | drug, liver, toxicity test, toxicity, drug development, tool development, liver toxicity, preclinical, model, induced pluripotent stem cell, liver cell, gene, immune response, computer model, outcome |
is listed by: Consortia-pedia is related to: Abbott Diagnostics is related to: Janssen Research and Development is related to: Merck is related to: Orion is related to: University of Liverpool; Liverpool; United Kingdom is related to: University of Freiburg; Baden-Wurttemberg; Germany is related to: German Cancer Research Center is related to: Karolinska Institute; Stockholm; Sweden is related to: University of Rennes 1; Rennes; France is related to: Leiden University; Leiden; Netherlands is related to: Utrecht University; Utrecht; Netherlands is related to: VU University; Amsterdam; Netherlands is related to: Cellartis is related to: CXR Biosciences is related to: Interface Europe is related to: KaLy-Cell is related to: Lhasa Limited is related to: SOLVO Biotechnology has parent organization: Interface Europe |
Innovative Medicines Initiative 115336; EFPIA |
nlx_158195 | SCR_003870 | Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury (MIP-DILI), Mechanism based Integrated systems for the Prediction of Drug Induced Liver Injury, Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury | 2026-08-29 11:21:41 | 2 | |||||||
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NEWMEDS Resource Report Resource Website 1+ mentions |
NEWMEDS (RRID:SCR_003872) | NEWMEDS | consortium, data or information resource, organization portal, portal | Consortium that will develop new models and methods to enable novel treatments for schizophrenia and depression including three important missing tools that will facilitate the translation of scientific findings into benefits for patients. The project will focus on developing new animal models which use brain recording and behavioral tests to identify innovative and effective drugs for schizophrenia. The project will develop standardized paradigms, acquisition and analysis techniques to apply brain imaging, especially fMRI and PET imaging to drug development. It will examine how new genetic findings (duplication and deletion or changes in genes) influence the response to various drugs and whether this information can be used to choose the right drug for the right patient. And finally, it will try and develop new approaches for shorter and more efficient trials of new medication - trials that may require fewer patients and give faster results. | drug, biomarker, neuroimaging, drug development, tool development, animal model, fmri, pet, gene, medicine, clinical trial, genetic variation, molecule, model, dna, protein |
is listed by: Consortia-pedia is related to: Abbott Diagnostics is related to: Janssen Research and Development is related to: Orion is related to: Pfizer Animal Genetics is related to: Roche is related to: King's College London; London; United Kingdom is related to: Karolinska Institute; Stockholm; Sweden is related to: University of Cambridge; Cambridge; United Kingdom is related to: Central Institute of Mental Health; Mannheim; Germany is related to: Spanish National Research Council; Madrid; Spain is related to: University of Manchester; Manchester; United Kingdom is related to: Bar-Ilan University; Ramat Gan; Isreal is related to: Psynova Neurotech is related to: deCODE genetics is related to: GABO:mi is related to: AbbVie has parent organization: King's College London; London; United Kingdom is parent organization of: DepressionTools.org Clinical Significance Calculator is parent organization of: Pharmacological Imaging and Pattern Recognition toolbox is parent organization of: DUPCheck |
Innovative Medicines Initiative 115008; EFPIA |
nlx_158196 | SCR_003872 | Novel Methods leading to New Medications in Depression and Schizophrenia, NEWMEDS - Novel Methods leading to New Medications in Depression and Schizophrenia | 2026-08-29 11:22:01 | 6 | |||||||
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AgedBrainSYSBIO Resource Report Resource Website 1+ mentions |
AgedBrainSYSBIO (RRID:SCR_003825) | AgedBrainSYSBIO | consortium, data or information resource, organization portal, portal | Consortium focused on identifying the foundational pathways responsible for the aging of the brain, with a focus on Late Onset Alzheimer's disease. They aim to identify the interactions through which the aging phenotype develops in normal and in disease conditions; modeling novel pathways and their evolutionary properties to design experiments that identify druggable targets. As early steps of neurodegenerative disorders are expected to impact synapse function the project will focus in particular on pre- or postsynaptic protein networks. The concept is to identify subsets of pathways with two unique druggable hallmarks, the validation of interactions occurring locally in subregions of neurons and a human and/or primate accelerated evolutionary signature. The consortium will do this through six approaches: * identification of interacting protein networks from recent Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) data, * experimental validation of interconnected networks working in subregion of a neuron (such as dendrites and dendritic spines), * inclusion of these experimentally validated networks in larger networks obtained from available databases to extend possible protein interactions, * identification of human and/or primate positive selection either in coding or in regulatory gene sequences, * manipulation of these human and/or primate accelerated evolutionary interacting proteins in human neurons derived from induced Pluripotent Stem Cells (iPSCs) * modeling predictions in drosophila and novel mouse transgenic models * validation of new druggable targets and markers as a proof-of-concept towards the prevention and cure of aging cognitive defects. The scientists will share results and know-how on Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) gene discovery, comparative functional genomics in mouse and drosophila models, in mouse transgenic approaches, research on human induced pluripotent stem cells (hiPSC) and their differentiation in vitro and modeling pathways with emphasis on comparative and evolutionary aspects. The four European small to medium size enterprises (SMEs) involved will bring their complementary expertise and will ensure translation of project results to clinical application. | consortium, drug, drug development, brain, phenotype, presynaptic, protein network, postsynaptic, systems biology, synapse, neuron, protein interaction, network, induced pluripotent stem cell, pathway, genome wide association study, cognitive defect, gene, protein |
is listed by: Consortia-pedia is related to: Pasteur Institute of Lille; Lille; France is related to: Mouse Clinical Institute; Alsace; France is related to: Hybrigenics is related to: Inserm Transfert is related to: VIB; Flanders; Belgium is related to: Quretec is related to: Gene Bridges is related to: European Bioinformatics Institute is related to: Tel Aviv University; Ramat Aviv; Israel is related to: SIB Swiss Institute of Bioinformatics is related to: Babraham Institute has parent organization: National Institute of Health and Medical Research; Rennes; France has parent organization: Inserm Transfert |
European Union FP7 305299 | nlx_158132 | SCR_003825 | 2026-08-29 11:22:00 | 3 | ||||||||
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BioSHaRE Resource Report Resource Website 10+ mentions |
BioSHaRE (RRID:SCR_003811) | BIOSHARE-EU | consortium, data or information resource, narrative resource, organization portal, portal, standard specification | A consortium of leading biobanks and international researchers from all domains of biobanking science to ensure the development of harmonized measures and standardized computing infrastructures enabling the effective pooling of data and key measures of life-style, social circumstances and environment, as well as critical sub-components of the phenotypes associated with common complex diseases. The overall aim is to build upon tools and methods available to achieve solutions for researchers to use pooled data from different cohort and biobank studies. This, in order to obtain the very large sample sizes needed to investigate current questions in multifactorial diseases, notably on gene-environment interactions. This aim will be achieved through the development of harmonization and standardization tools, implementation of these tools and demonstration of their applicability. BioSHaRE researchers are collaborating with P3G, the Global Alliance for Genomics and Health, IRDiRC (International Rare Diseases Research Consortium), H3Africa and other organizations on the development of an International Code of Conduct for Genomic and Health-Related Data Sharing. A draft version is available for external review. Generic documents have been prepared covering areas of biobanking that are of major importance. SOPs have been finalized for blood withdrawal (SOPWP5001blood withdrawal), manual blood processing (SOPWP5002blood processing), shipping of biosamples (SOPWP5003shipping) and withdrawal, processing and storage of urine samples (SOPWP5004urine). | gene-environment interaction, life-style, social circumstance, environment, phenotype, disease, biobank, socio-economic factor, data sharing, gene, clinical |
is listed by: Consortia-pedia has parent organization: University of Groningen; Groningen; Netherlands is parent organization of: BioResource Impact Factor |
European Union FP7 | nlx_158110 | SCR_003811 | Biobank Standardisation and Harmonisation for Research Excellence, Biobank Standardisation and Harmonisation for Research Excellence in the European Union | 2026-08-29 11:21:39 | 22 | |||||||
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FlexGen Resource Report Resource Website 1+ mentions |
FlexGen (RRID:SCR_003902) | FlexGen | commercial organization | A biotechnology company that has developed technology for synthesizing custom microarrays, the FlexArrayer. Its is a desk-top sized instrument which allows the researcher to generate, in their own laboratory, either a custom oligonucleotide array in a single day or oligonucleotide pool in a few days. Recent developments in synthesis chemistry allows many modifications to be incorporated or for alternative chemistries to be considered., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | biotechnology, microarray, custom oligonucleotide array, oligonucleotide pool, oligonucleotide, gene, probe synthesis, target enrichment, probe design, biomolecule, dna sequencing, oligonucleotide synthesis, re-sequencing | is related to: READNA | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158237 | SCR_003902 | FlexGen B.V. | 2026-08-29 11:21:47 | 6 | |||||||
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Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations Resource Report Resource Website |
Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations (RRID:SCR_004019) | BATTER-UP | data or information resource, portal, topical portal | A consortium evaluating a new biomarker screening test that might help identify patients with rheumatoid arthritis (RA) who are unlikely to benefit from anti-tumor necrosis factor-alpha (TNFalpha) medications. BATTER-UP will enroll around 1,000 patients being treated by one of several marketed anti-TNF RA drugs: Enbrel, Remicade, Humira, Simponi, or Cimzia. Through data analyses and predictive response modeling, the consortium aims to better understand which patients with RA will derive the greatest benefit from TNF inhibitors. The investigators in this observational study will attempt to validate an 8-gene biomarker set based on work by Biogen Idec researchers as likely to predict anti-TNF responsiveness in patients with RA. In preliminary results, the 8-gene biomarker set predicted with 89% accuracy individuals who did not reach European League Against Rheumatism (EULAR) Disease Activity Score (DAS)-28 good response after 14 weeks of treatment. The 8 genes included in the screen are CLTB, MXRA7, CXorf52, COL4A3BP, YIPF6, FAM44A, SFRS2, and PGK1. Biological samples and clinical outcome information will be used to confirm and extend the utility of previously published biomarkers that can predict response to anti-TNF agents. These data may also generate new hypotheses for further testing. The BATTER-UP samples and data will be established as a reference set for investigation of personalized medicine in RA. The study will be a resource of DNA and other biological materials that can be investigated for biomarkers in the future as new technologies arise. | anti-tumor necrosis factor-alpha, gene, biomarker, drug development, basic research, personalized medicine, enbrel, remicade, humira, simponi, cimzia, cltb, mxra7, cxorf52, col4a3bp, yipf6, fam44a, sfrs2, pgk1, clinical, dna, serum, plasma, rna, whole blood |
uses: ClinicalTrials.gov is listed by: Consortia-pedia is related to: Feinstein Institute for Medical Research has parent organization: Feinstein Institute for Medical Research has parent organization: ClinicalTrials.gov |
Biogen Idec ; Bristol-Myers Squibb ; Centocor ; Crescendo Bioscience ; Genentech ; Medco Health Solutions ; Regeneron Pharmaceuticals ; Sanofi-Aventis |
nlx_158440 | SCR_004019 | Biomarkers of Anti-TNF-alpha Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients, Biomarkers of Anti-TNF- Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients (BATTER-UP), Biomarkers of Anti-TNF- Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients | 2026-08-29 11:22:03 | 0 | |||||||
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GeneCommittee Resource Report Resource Website |
GeneCommittee (RRID:SCR_004168) | geneCommittee | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research. | dna, microarray, rna-seq, gene expression, classification, gene set, gene, gene set enrichment, functional annotation |
is listed by: OMICtools has parent organization: University of Vigo; Galicia; Spain |
PMID:24475928 | Acknowledgement requested | OMICS_02291 | https://github.com/michada/GeneCommittee | SCR_004168 | 2026-08-29 11:21:49 | 0 | ||||||
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HLASeq Resource Report Resource Website |
HLASeq (RRID:SCR_004185) | HLASeq | software resource | An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data. | genotyping, hla, next generation sequencing, gene, command-line, python |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01543 | SCR_004185 | 2026-08-29 11:22:05 | 0 | ||||||||
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BrainSpan Resource Report Resource Website 1+ mentions |
BrainSpan (RRID:SCR_004219) | atlas, data or information resource, expression atlas | Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis. | brain, development, brain development, exon, microarray, gene, rna-seq, expression value, expression |
is used by: NIF Data Federation has parent organization: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) |
Free, Freely available | nlx_98194, nlx_86215, SCR_004877, SCR_005029, SCR_004344, nlx_37081, nlx_2397 | http://brainspan.org/rnaseq/downloads.html?format=html, http://brainspan.org/docs.html | http://brainspan.org/docs.html | SCR_004219 | BrainSpan: RNA-Seq exons, BrainSpan - Exon microarray summarized to genes | 2026-08-29 11:21:49 | 3 | ||||||
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TAGS Resource Report Resource Website 100+ mentions |
TAGS (RRID:SCR_004294) | TAGS | data analysis software, data processing software, software application, software resource, time-series analysis software | Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, enrichment analysis, time series, function, structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tags, nlx_31187 | https://bio.tools/tags | http://166.111.130.26/member/yliu/TAGS/ | SCR_004294 | 2026-08-29 11:22:00 | 139 | ||||||
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dkCOIN Resource Report Resource Website 1+ mentions |
dkCOIN (RRID:SCR_004438) | dkCOIN | data or information resource, database, resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO). | gene, adenovirus construct, antibody, co-immunoprecipitation, embryonic stem cell line, functional genomics, histology, mouse strain, pcr primer, protocol, real time pcr, metadata, diabetes, stem cell, metabolism, tissue development, web service, cloud, embryonic stem cell |
is used by: NIF Data Federation is related to: Beta Cell Biology Consortium is related to: NIDDK Information Network (dkNET) is related to: National Mouse Metabolic Phenotyping Centers is related to: Nuclear Receptor Signaling Atlas is related to: Diabetic Complications Consortium is related to: T1DBase is related to: OBO has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
NIDDK 3U01DK072473-05S3; NIDDK 5U24DK076169; NIDDK U19DK062434 |
PMID:22734043 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44256 | SCR_004438 | NIDDKConsortium Interconnectivity Network | 2026-08-29 11:22:07 | 1 | |||||
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NEXTDB Resource Report Resource Website 10+ mentions |
NEXTDB (RRID:SCR_004480) | NextDB | analysis service resource, atlas, data analysis service, data or information resource, database, expression atlas, production service resource, service resource | Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae | rnai phenotype, homology, blast, fasta, chromosome map, cosmid, gene, cdna clone, genome, in situ hybridization, expressed sequence tag, developmental stage, sequence, embryonic caenorhabditis elegans, chromosome, phenotype, blastx, clone, sequence tag, yac, predicted gene, protein, development, larval caenorhabditis elegans, image collection, experimental protocol, FASEB list |
is related to: Expression Patterns for C. elegans promoter GFP fusions is related to: Expression Patterns for C. elegans promoter GFP fusions has parent organization: National Institute of Genetics; Shizuoka; Japan |
Core Research for Evolutional Science and Technology ; Japan Science and Technology Corporation ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
Permission required, Acknowledgement required | nlx_46406 | SCR_004480 | Nematode Expression Pattern DataBase | 2026-08-29 11:22:08 | 35 | ||||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | analysis service resource, data or information resource, data repository, data set, database, production service resource, service resource, software resource, source code, storage service resource | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-08-29 11:21:53 | 2 |
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