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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BrainSpan Resource Report Resource Website 1+ mentions |
BrainSpan (RRID:SCR_004219) | expression atlas, atlas, data or information resource | 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 | 2026-08-04 09:41:05 | 2 | ||||||
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TAGS Resource Report Resource Website 100+ mentions |
TAGS (RRID:SCR_004294) | TAGS | data processing software, data analysis software, time-series analysis software, software resource, software application | 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 | 2026-08-04 09:41:06 | 139 | ||||||
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NEXTDB Resource Report Resource Website 10+ mentions |
NEXTDB (RRID:SCR_004480) | NextDB | data analysis service, analysis service resource, expression atlas, production service resource, service resource, atlas, database, data or information 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 | 2026-08-04 09:41:10 | 35 | ||||||
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HAP-SAMPLE Resource Report Resource Website 1+ mentions |
HAP-SAMPLE (RRID:SCR_009234) | HAP-SAMPLE | data analysis service, analysis service resource, software resource, software application, production service resource, service resource | Web application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be genotyped, along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans. (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | nlx_154392 | SCR_009234 | 2026-08-04 09:42:19 | 4 | |||||||||
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R/QTLBIM Resource Report Resource Website 1+ mentions |
R/QTLBIM (RRID:SCR_009375) | software application, software toolkit, software resource, software library | Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154597, biotools:qtlbim | http://www.ssg.uab.edu/qtlbim/index.jsp, https://cran.r-project.org/src/contrib/Archive/qtlbim/, https://bio.tools/qtlbim | http://www.qtlbim.org/ | SCR_009375 | 2026-08-04 09:42:22 | 2 | ||||||||
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Renal Disease Portal Resource Report Resource Website |
Renal Disease Portal (RRID:SCR_009030) | Renal Disease Portal | portal, data set, topical portal, disease-related portal, data or information resource | An integrated resource for information on genes, QTLs and strains associated with a variety of kidney and renal system conditions such as Renal Hypertension, Polycystic Kidney Disease and Renal Insufficiency, as well as Kidney Neoplasms. | gene, quantitative trait locus, strain, renal hypertension, kidney neoplasm, phenotype, pathway, biological process, disease, kidney, genome, gviewer, chromosome, molecular function, cellular component, visualization, synteny |
is related to: NIDDK Information Network (dkNET) is related to: Gene Ontology has parent organization: Rat Genome Database (RGD) |
Renal disease, Renal hypertension, Polycystic kidney disease, Renal insufficiency, Kidney neoplasm, Diabetes Insipidus, Hyperoxaluria, Renal hypertension, Nephritis, Nephrocalcinosis, Nephrolithiasis, Nephrosis, Renal Fibrosis, Inborn Error of Renal Tubular Transport, Uremia | nlx_153941 | SCR_009030 | RGD Renal Disease Portal | 2026-08-04 09:42:17 | 0 | |||||||
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Digital Ageing Atlas Resource Report Resource Website 10+ mentions |
Digital Ageing Atlas (RRID:SCR_009020) | DAA | storage service resource, data repository, service resource, database, data or information resource | Database of age-related changes covering different biological levels, including molecular, physiological, psychological and pathological age-related data, to create an interactive portal that serves as a centralized collection of human aging changes and pathologies. To facilitate integrative, system-level studies of aging, the DAA provides a centralized source for aging-related data as well as basic tools to query and visualize the data, including anatomical models. Data in the DAA is manually curated from the literature and retrieved from public databases. For more detailed analyses users are able to download the entire database. More information on how to use the DAA is available on the help page. The DAA primarily focuses on human aging, but also includes supplementary mouse data, in particular gene expression data, to enhance and expand the information on human aging. If you would like to contribute to the database yourself, for instance if you have new data on aging, please use the contribute page to submit your data. | late adult human, anatomy, gene, molecular, pathological, physiological, psychological, tissue, reference, cellualar, gene expression | has parent organization: University of Liverpool; Liverpool; United Kingdom | Aging | The community can contribute to this resource, Creative Commons Attribution License, v3 Unported | nlx_153874 | SCR_009020 | Digital Aging Atlas | 2026-08-04 09:42:17 | 12 | ||||||
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MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data processing software, software application, software resource, data analysis software | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach, https://bio.tools/mach | https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | mach2qtl, MaCH | 2026-08-04 09:42:26 | 925 | |||||
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Leaf Senescence Database Resource Report Resource Website 1+ mentions |
Leaf Senescence Database (RRID:SCR_010227) | LSD | storage service resource, data repository, service resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26, 2019. Database of leaf senescence to collect SAGs, mutants, phenotypes and literature references. Leaf senescence has been recognized as the last phase of plant development, a highly ordered process regulated by genes called SAGs. By integrating the data from mutant studies and transgenic analysis, they collected many SAGs related to regulation of the leaf senescence in various species. Additionally, they have categorized SAGs according to their functions in regulation of leaf senescence and used standard criteria to describe senescence associated phenotypes for mutants. Users are welcome to submit the new SAGs. | gene, mutant, leaf, phenotype, blast, plant development, sag | has parent organization: Peking University; Beijing; China | Senescence, Aging | Postdoctoral Fellowship at Peking-Tsinghua Center for Life Sciences ; Ministry of Science and Technology of China 2009CB119101; Ministry of Agriculture of China 2010ZX08010-002; Natural Science Foundation of China 31071160; China Postdoctoral Science Foundation 2012M520108; China Postdoctoral Science Foundation 2013T60031 |
PMID:24185698 PMID:21097471 |
THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_156775 | SCR_010227 | 2026-08-04 09:42:36 | 7 | |||||
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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data processing software, software application, software resource, data analysis software | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-08-04 09:42:49 | 24583 | ||||||
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Algal Functional Annotation Tool Resource Report Resource Website |
Algal Functional Annotation Tool (RRID:SCR_012034) | Algal Functional Annotation Tool | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest. | gene, pathway, visualization, annotation, function, protein family, ontology, protein, genomics |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: MetaCyc is related to: Reactome is related to: Pfam is related to: InterPro has parent organization: University of California at Los Angeles; California; USA |
DOE ; NAABB ; IGP ; Air Force Office of Scientific Research |
PMID:21749710 | OMICS_02226 | SCR_012034 | 2026-08-04 09:42:53 | 0 | |||||||
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Zebra Finch Expression Brain Atlas Resource Report Resource Website 10+ mentions |
Zebra Finch Expression Brain Atlas (RRID:SCR_012988) | ZEBrA | expression atlas, atlas, database, data or information resource | Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches. | gene, expression, brain, in-situ, hybridization, taeniopygia, vocal learning, anatomical, atlas, data set, molecular neuroanatomy, adult, male, gene, image, bird, image, avian | has parent organization: Oregon Health and Science University; Oregon; USA | NINDS R03 NS059755; NIGMS R24 GM092842 |
Free, Freely available | nif-0000-24345, SCR_000641, nlx_152091 | http://ignrhnet.ohsu.edu/finch/songbird/index.php | SCR_012988 | zebra, , Zebra Finch Expression Brain Atlas, atlas, Zebra Finch Brain Atlas, ZEBrA, finch | 2026-08-04 09:43:07 | 38 | |||||
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Virus Pathogen Resource (ViPR) Resource Report Resource Website 100+ mentions |
Virus Pathogen Resource (ViPR) (RRID:SCR_012983) | ViPR | data processing software, storage service resource, software resource, software application, data repository, service resource, data visualization software, database, data or information resource | Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research. | flu, gene, bioinformatic, database, diagnostic, genomic, health, human, influenza, pathogen, protein, research, strain, therapeutic, tool, vaccine, virus, visualization, FASEB list |
is recommended by: National Library of Medicine is listed by: Data and Computational Resources to Address COVID-19 is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of Texas Southwestern Medical Center; Texas; USA |
COVID-19 | NIAID | Restricted | nif-0000-25312, DOI:10.35083, DOI:10.35084, DOI:10.17616/R30P93, DOI:10.25504/FAIRsharing.2qx8n8 | http://www.viprbrc.org/, https://doi.org/10.17616/r30p93, https://doi.org/10.35083/, https://doi.org/10.35084/, https://dx.doi.org/10.35083/, https://dx.doi.org/10.35084/, https://fairsharing.org/10.25504/FAIRsharing.2qx8n8 | SCR_012983 | Virus Pathogen Resource, ViPR | 2026-08-04 09:43:07 | 140 | ||||
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edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | data processing software, software application, software resource, data analysis software | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
NHMRC 406657; Independent Research Institutes Infrastructure Support Scheme 361646; Victorian State Government OIS grant ; Melbourne International Research Scholarship ; Harris and IBS Honours scholarships |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-08-04 09:43:05 | 21899 | ||||
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KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | data analysis service, portal, analysis service resource, web service, topical portal, software resource, data access protocol, production service resource, service resource, database, data or information resource | Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. | model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell |
is used by: NIF Data Federation is used by: Arabidopsis Reactome is used by: LIPID MAPS Proteome Database is used by: globaltest is used by: MitoMiner is used by: Database for Annotation Visualization and Integrated Discovery is used by: Biochemical Pathways Reaction Kinetics Database is used by: Ultimate Rough Aggregation of Metabolic Map is used by: GEMINI is used by: In vivo - In silico Metabolite Database is listed by: 3DVC is listed by: OMICtools is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database is related to: PathCase Pathways Database System is related to: ExplorEnz is related to: NCBI BioSystems Database is related to: Allen Institute Neurowiki is related to: eQuilibrator is related to: GeneTrail is related to: KegTools is related to: PRODORIC is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: METLIN is related to: Kidney and Urinary Pathway Knowledge Base is related to: DAVID is related to: ConsensusPathDB is related to: ENZYME is related to: FlyMine is related to: Babelomics is related to: SynSysNet is related to: Cotton EST Database is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: INMEX is related to: BioExtract is related to: ClueGO is related to: MalaCards is related to: TrED is related to: FunTree is related to: MOPED - Model Organism Protein Expression Database is related to: ProOpDB is related to: KOBAS is related to: GeneTerm Linker is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: GeneCodis is related to: FunNet - Transcriptional Networks Analysis is related to: LegumeIP is related to: Algal Functional Annotation Tool is related to: aGEM is related to: DINIES is related to: KEGG PATHWAY Database is related to: ShinyGO is related to: KEGGREST has parent organization: Kyoto University; Kyoto; Japan has parent organization: University of Tokyo; Tokyo; Japan is parent organization of: KegTools works with: DIANA-mirPath works with: MiMeDB |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:22700311 PMID:22130871 PMID:22080510 PMID:19880382 PMID:19172790 PMID:18428742 PMID:18287706 PMID:18077471 PMID:16381885 PMID:16014746 PMID:14681412 PMID:12539951 PMID:11752249 PMID:10928937 PMID:10592173 PMID:9847135 |
Restricted | nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 | http://www.genome.jp/kegg/ | SCR_012773 | KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes | 2026-08-04 09:43:05 | 75877 | ||||
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Sequencing of Candida Albicans Resource Report Resource Website 10+ mentions |
Sequencing of Candida Albicans (RRID:SCR_013437) | topical portal, portal, data or information resource | The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects. | stanford, genome, technology, shotgun, sequencing, strain, haploid, gene, nucleation, health, life, aids, drug, patient | has parent organization: Stanford University; Stanford; California | Burroughs Wellcome Fund ; NIDCR DE12302-02S2; NIAID RO1AI16567; NIAID RO1AI46351; NIAID NO1AI05406; NIDCR R01DE12940; NIDCR P01DE07946 |
nif-0000-30294 | SCR_013437 | Candida Albicans | 2026-08-04 09:43:13 | 21 | ||||||||
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L2L Microarray Analysis Tool Resource Report Resource Website 1+ mentions |
L2L Microarray Analysis Tool (RRID:SCR_013440) | L2L | data analysis service, data processing software, analysis service resource, data analysis software, storage service resource, software resource, software application, production service resource, service resource, data repository, database, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019. Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible |
microarray, gene expression, adipogenesis, biological, biological process, cancer, cell cycle regulator, cellular component, chromatin, cockayne syndrome, dna damage, growth factor, hormone, human biology, hypoxic response, immune mediator, inflammatory mediator, molecular function, molecular neuroanatomy resource, adipocyte, development, hypoxia, immune, inflammation, metabolism, mitogen, neuro, rna, vascular, transcription, tissue, splicing, mouse, human, rat, source code, statistical analysis, gene, chromatin structure |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Washington; Seattle; USA |
Cockayne syndrome, DNA damage, Other, Aging, Cancer | Cora May Poncin Foundation ; NIGMS GM41624 |
PMID:16168088 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10463 | http://depts.washington.edu/l2l/about.html | SCR_013440 | L2L Microarray Database, L2L Microarray Analysis Tool: A simple tool for discovering the hidden biological significance in microarray expression data, L2L MDB | 2026-08-04 09:43:13 | 1 | |||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | data analysis service, analysis service resource, web service, storage service resource, software resource, data access protocol, production service resource, service resource, data repository, database, data or information resource | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-08-04 09:43:11 | 1239 | ||||||
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PiGenome Resource Report Resource Website |
PiGenome (RRID:SCR_013394) | PiGenome | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6. | gene expression, genome, sequence, gene, expressed sequence tag, consensus sequence, bac clone, bac end sequence, bac contig, quantitative trait loci, singleton, marker, unigene, chromosome 6, blast, transcript, bacterial artificial chromosome, snp, alignment |
is related to: Gene Ontology has parent organization: National Institute of Animal Science; Gyeonggi-do; South Korea |
National Institute of Animal Science; Gyeonggi-do; Korea ; Korean Rural Development Administration ; Biogreen21 Project 20050301034467 |
PMID:19082661 | nlx_153888 | http://pigenome.nabc.go.kr/ | SCR_013394 | Sus scrofa Genome database, Pig Genome Database, Pigenome database | 2026-08-04 09:43:12 | 0 | |||||
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GeneSigDB Resource Report Resource Website 10+ mentions |
GeneSigDB (RRID:SCR_013275) | GeneSigDB | data analysis service, analysis service resource, web service, storage service resource, software resource, data access protocol, production service resource, service resource, data repository, database, data or information resource | Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service. | gene, gene signature, curated gene signature, gene expression, gene expression signature, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: Computational Biology and Functional Genomics Laboratory at Harvard |
Cancer | Genome Research Institute ; Dana-Farber Cancer Institute ; Women's Cancers Program ; Claudia Adams Barr Foundation ; NLM 1R01 LM010129; NCI 1U19 CA148065; NHGRI 1P50 HG004233 |
PMID:22110038 | biotools:genesigdb, nlx_149342 | https://bio.tools/genesigdb | SCR_013275 | Gene Signature Data Base, GeneSigDB - Curated Gene Signatures Database | 2026-08-04 09:43:10 | 24 |
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