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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Quantitative Enrichment of Sequence Tags Resource Report Resource Website 10+ mentions |
Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) | QuEST | software resource | A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments. | genome-wide, transcription factor binding site, chip-seq, transcription factor, binding site, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Stanford University; Stanford; California |
PMID:19160518 | OMICS_00458, biotools:quest | https://bio.tools/quest | SCR_004065 | Quantitative Enrichment of Sequence Tags: QuEST | 2026-10-17 01:26:08 | 49 | ||||||
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Neural-Immune Gene Ontology Resource Report Resource Website 1+ mentions |
Neural-Immune Gene Ontology (RRID:SCR_004120) | NIGO | controlled vocabulary, data or information resource, ontology | Ontology that is a subset of GO directed for neurological and immunological systems. It was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains. | obo |
is listed by: BioPortal is related to: Gene Ontology |
nlx_157506 | SCR_004120 | 2026-10-17 01:25:50 | 1 | |||||||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | d spatial image, data or information resource, data repository, database, image collection, service resource, storage service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-10-17 01:26:56 | 7 | |||||
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Network Analysis, Visualization and Graphing TORonto Resource Report Resource Website 50+ mentions |
Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) | NAViGaTOR | d visualization software, data processing software, data visualization software, software application, software resource | A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches. | fly, algorithm, capacity, graphical, graphing, human, interaction, interactome, intersection, mouse, network, node, protein, proteomic, rat, worm, yeast, graphing application, 2d visualization, 3d visualization, visualization, biological network, protein-protein interaction, gene, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Genomics Institute ; Canada Research Chair Program ; Ontario Research Fund Research Excellence ; Canada Foundation for Innovation 12301; Canada Foundation for Innovation 203383 |
PMID:19837718 | Freely-downloadable for academic and not-for-profit institutions | nif-0000-25610, biotools:navigator | https://bio.tools/navigator | SCR_008373 | NAViGaTOR - Network Analysis Visualization and Graphing TORonto, NAViGaTOR - Network Analysis Visualization & Graphing TORonto | 2026-10-17 01:27:17 | 55 | ||||
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bio.tools Resource Report Resource Website 10+ mentions |
bio.tools (RRID:SCR_014695) | catalog, data or information resource, database, software repository, software resource | Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information. | Registry, software registry, biological tool, data services registry, services discovery portal, bio.tools |
lists: FACS lists: Fusion Analyser lists: AffyRNADegradation lists: GUARDD lists: GEOquery lists: RNAcontext lists: Patchwork lists: SODOCK lists: MIMOSA lists: GraBCas lists: SNAVI lists: GENIE3 lists: Megraft lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: PeptideProphet lists: Quant lists: VARiD lists: ProteinProphet lists: Flicker lists: ARACHNE lists: Micro-Analyzer lists: riboPicker lists: dbSTS lists: POPBAM lists: flowPeaks lists: cn.FARMS lists: Sequence Search and Alignment by Hashing Algorithm lists: SAMBLASTER lists: Pindel lists: Mfuzz lists: TAPyR lists: ContEst lists: PGS lists: PEPPER lists: FPSAC lists: FlipFlop lists: ProGlycProt lists: MuTect lists: TriageTools lists: BLASR lists: DSRC lists: SRMA lists: Bowtie lists: StringTie lists: PhenoFam lists: SOAP lists: SplitSeek lists: MUSCLE lists: SplicePlot lists: Illuminator lists: GimmeMotifs lists: Skylign lists: BreakSeq lists: Barrnap lists: SLOPE lists: CUDA-EC lists: QualiMap lists: massiR lists: OmicsOffice for NGS SeqSolve lists: QUAST lists: GenomicTools lists: NGSUtils lists: TileQC lists: Sequedex lists: PARalyzer lists: BFCounter lists: TALLYMER lists: SNPchip lists: VAAL lists: ProbRNA lists: ADMIXTURE lists: SABER lists: piCALL lists: CYCLE lists: limmaGUI lists: DEXUS lists: KAnalyze lists: BeadDataPackR lists: wateRmelon lists: NGSrich lists: OLIN lists: fRMA lists: MACAT lists: affylmGUI lists: DictyOGlyc lists: GlyProt lists: CisGenome lists: ToppCluster lists: AnimalTFDB lists: oneChannelGUI lists: YinOYang lists: Chilibot: Gene and Protein relationships from MEDLINE lists: asSeq lists: FARMS lists: GERMLINE lists: unifiedWMWqPCR lists: HAPLOPAINTER lists: Biocatalogue - The Life Science Web Services Registry lists: HOMOZYGOSITYMAPPER lists: MetaBase lists: PyLOH lists: InterMine lists: myExperiment lists: pRESTO lists: TANGO lists: Prediction of Amyloid Structure Aggregation lists: PhosphoSitePlus: Protein Modification Site lists: CCAT lists: BREAKDANCER lists: FACTA+. lists: PEDIGRAPH lists: CQN lists: CanSNPer lists: SamSPECTRAL lists: TEMP lists: MEME Suite - Motif-based sequence analysis tools lists: SNPAAMapper lists: Pecan lists: InteroPorc lists: AffyPipe lists: ADaCGH2 lists: DINDEL lists: ASPGD lists: Candida Genome Database lists: BISC lists: PurBayes lists: SNVer lists: Cake lists: S-MART lists: SHORTY lists: Pathway Commons lists: TcoF lists: BEETL-fastq lists: SBARS lists: cpnDB: A Chaperonin Database lists: cisRED: cis-regulatory element lists: FlyFactorSurvey lists: pymzML lists: EchoBASE lists: Blood Group Antigen Gene Mutation Database lists: WebGeSTer DB lists: RUbioSeq lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: MethylAid lists: ExomeDepth lists: ZOOM lists: Iterative Signature Algorithm lists: ShotGun lists: Pathview lists: T3DB lists: Autophagy Database lists: rBiopaxParser lists: QualitySNPng lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: libCSAM lists: RopeBWT2 lists: NetPathMiner lists: BioNumbers lists: leeHom lists: tweeDEseq lists: ProRata lists: Coding Potential Calculator lists: CPTRA lists: MFEprimer lists: Distant Regulatory Elements lists: HGNC lists: GATE lists: SuperPred: Drug classification and target prediction lists: hot scan lists: AltAnalyze - Alternative Splicing Analysis Tool lists: Primer3Plus lists: pairheatmap lists: BioJS lists: ms lims lists: Eukaryotic Linear Motif lists: Proteome Analyst Specialized Subcellular Localization Server lists: HYDEN lists: drFAST lists: GeneFisher lists: GreenPhylDB lists: MiST - Microbial Signal Transduction database lists: Pipeliner lists: Gene Set Enrichment Analysis lists: Piano lists: Weighted Gene Co-expression Network Analysis lists: FastSNP lists: Triplex lists: mrsFAST lists: GenePattern lists: NovelSeq lists: QDNAseq lists: MutDB lists: SplicingCompass lists: deFuse lists: Database of Interacting Proteins (DIP) lists: Assembly Based ReAligner lists: MAGE-TAB lists: ggbio lists: miR-PREFeR lists: NanoStringNorm lists: MIPgen lists: HTqPCR lists: Parseq lists: T-profiler lists: Bpipe lists: jmzTab lists: L-Measure lists: Snakemake lists: PoPoolation lists: MultiPhen lists: PheWAS R Package lists: Quantitative Enrichment of Sequence Tags lists: ALDEx2 lists: INMEX lists: InsertionMapper lists: BSRD lists: SeWeR - SEquence analysis using WEb Resources lists: Segway - a way to segment the genome lists: Stem Cell Discovery Engine lists: TagDust lists: Kdetrees lists: Tree and reticulogram REConstruction lists: NEWT lists: DER Finder lists: BioPig lists: Selectome: a Database of Positive Selection lists: Distributed String Mining Framework lists: PILGRM lists: Apo and Holo structures DataBase lists: MLTreeMap lists: MG-RAST lists: miRNAKey lists: SVseq lists: Small Molecule Pathway Database lists: Information Hyperlinked Over Proteins lists: SVMerge lists: BioSample Database at EBI lists: MetaPhyler lists: SOPRA lists: NCBI BioSystems Database lists: SLIQ lists: G-BLASTN lists: SSPACE lists: AmphoraNet lists: NCBI Structure: Cn3D lists: DELLY lists: RUM lists: STING Report lists: SoyBase lists: SINA lists: Strelka2 lists: RNA-eXpress lists: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets lists: VFS lists: ShoRAH lists: READSCAN lists: ERANGE lists: GeneTalk lists: ORMAN lists: SEECER lists: Scripture lists: SPOT - Biological prioritization after a SNP association study lists: NCBO Annotator lists: CoPub lists: SolexaQA lists: PHAge Search Tool lists: Knime4Bio lists: MethPipe lists: Bis-SNP lists: GobyWeb lists: EMAGE Gene Expression Database lists: FusionMap lists: Yabi lists: GSNAP lists: rQuant lists: MethylViewer lists: DistMap lists: PASS lists: mrFAST lists: Kismeth lists: Stampy lists: TreQ lists: FLASH lists: SAMStat lists: PRINSEQ lists: MethylomeDB lists: SOAPaligner/soap2 lists: TMA Navigator lists: TRANSFAC lists: SeqMap lists: Bambino lists: MicrobesOnline lists: DMRforPairs lists: TIGRFAMS lists: CLIPZ lists: SNPsandGO lists: ToppGene Suite lists: SeqTrace lists: GoSurfer lists: Jellyfish lists: GoFish lists: WEGO - Web Gene Ontology Annotation Plot lists: ngsTools lists: GraphProt lists: SerbGO lists: GoPubMed lists: ccPDB - Compilation and Creation of datasets from PDB lists: DOMMINO - Database Of MacroMolecular INteractiOns lists: SOURCE lists: DistiLD - Diseases and Traits in LD lists: PePr lists: Expression Profiler lists: eQuilibrator lists: DiseaseMeth lists: Dr.VIS - Human Disease-Related Viral Integration Sites lists: FunTree lists: DBETH - Database for Bacterial ExoToxins for Humans lists: BLESS lists: GWASdb lists: HFV Database lists: IndelFR - Indel Flanking Region Database lists: MIPModDB lists: Europe PubMed Central lists: CharProtDB: Characterized Protein Database lists: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature lists: MMMDB - Mouse Multiple tissue Metabolome DataBase lists: ICEberg lists: VirHostNet: Virus-Host Network lists: Cascade lists: Polbase lists: VIRsiRNAdb lists: 959 Nematode Genomes lists: OGEE - Online GEne Essentiality database lists: ProPortal lists: SNPedia lists: Newtomics lists: HotRegion - A Database of Cooperative Hotspots lists: SitEx lists: ScerTF lists: HMM-TM lists: NRG-CING lists: PRED-LIPO lists: InterEvol database lists: SpliceDisease lists: RNA CoSSMos lists: deepSNV lists: PRED-GPCR lists: RecountDB lists: VICUNA lists: ProRepeat lists: MouseBook lists: COEUS lists: Predictive Networks lists: PRED-SIGNAL lists: Flycircuit lists: COLT-Cancer lists: ATRHUNTER lists: GeneTrail lists: epigenomix lists: Pseudomonas Genome Database lists: QCGWAS lists: TSSer lists: UMD-BRCA1/ BRCA2 databases lists: PomBase lists: Phytozome lists: OMPdb lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: MSIsensor lists: GWAMA lists: SpliceTrap lists: ViralZone lists: waviCGH lists: MyHits lists: Decombinator lists: CAPS Database lists: ADGO lists: zfishbook lists: EagleView lists: Gene Expression Database lists: SRAdb lists: BEDTools lists: IMGT/GENE-DB lists: RamiGO lists: canSAR lists: IMGT/LIGM-DB lists: PLEXdb - Plant Expression Database lists: COHCAP lists: DARC - Database for Aligned Ribosomal Complexes lists: Immune Epitope Database and Analysis Resource (IEDB) lists: AutismKB lists: RIKEN integrated database of mammals lists: Myrna lists: PhenoM - Phenomics of yeast Mutants lists: BIGpre lists: HIstome: The Histone Infobase lists: TriTrypDB lists: CuticleDB lists: Midbody, Centrosome and Kinetochore lists: SCOP: Structural Classification of Proteins lists: Expression Database in 4D lists: VIDA lists: Database of Arabidopsis Transcription Factors lists: Atlas of Genetics and Cytogenetics in Oncology and Haematology lists: ESEfinder 3.0 lists: agriGO lists: Taipan lists: AgBase lists: Chromosome 7 Annotation Project lists: MEROPS lists: T1DBase lists: Hyper Cell Line Database lists: GenoTan lists: VISTA Browser lists: lobSTR lists: Candidate Genes to Inherited Diseases lists: VISTA Enhancer Browser lists: Gene Array Analyzer lists: Network Analysis, Visualization and Graphing TORonto lists: MuSiC lists: MfunGD - MIPS Mouse Functional Genome Database lists: eTBlast lists: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) lists: FGDP lists: hiPathDB - human integrated Pathway DB with facile visualization lists: miRNEST lists: neXtProt lists: NetOGlyc lists: QuasiRecomb lists: GMAP lists: iMir lists: MaCH-Admix lists: SeqBuster lists: LegumeIP lists: DNAtraffic lists: MicroSNiPer lists: Pathema lists: BeeBase lists: Geneious lists: MOSCPHASER lists: SNPinfo Web Server lists: elastix lists: MIRA lists: NEBcutter lists: CopySeq lists: CUPSAT lists: Atlas2 lists: ALLPATHS-LG lists: Velvet lists: HomSI lists: SVDetect lists: omiRas lists: HMCan lists: HapFABIA lists: WEBLOGO lists: ZINBA lists: SICER lists: kmer-SVM lists: MAnorm lists: Pedimap lists: nucleR lists: CEQer lists: MutSig lists: DIANA-LncBase lists: MethMarker lists: PeakRanger lists: PlnTFDB lists: CloudBurst lists: NPS lists: MutationTaster lists: ProDesign lists: OligoArray lists: ArrayAnalysis.org lists: PatMaN lists: SEAL lists: Asterias lists: RACE lists: RobiNA lists: CANGS lists: PlantTFcat lists: LitInspector lists: HSLPred lists: PSAR-Align lists: CancerResource lists: JiffyNet lists: ECHO lists: GPU-Meta-Storms lists: GenoREAD lists: TopHat-Fusion lists: GeneStitch lists: FABIA lists: CPFP lists: MFPaQ lists: ICPL ESIQuant lists: easyRNASeq lists: PREDDIMER lists: NetCoffee lists: SlideSort-BPR lists: miRPlant lists: AlienTrimmer lists: PRIDE Converter 2 lists: SNP ratio test lists: compomics-utilities lists: Allim lists: PLEK lists: ISDTool lists: OBI-Warp lists: LocalAli lists: iceLogo lists: multiplierz lists: AMS lists: NGSmethDB lists: PoolHap lists: DNaseR lists: Btrim lists: COBRApy lists: NAIL lists: CAZy- Carbohydrate Active Enzyme lists: A5-miseq lists: ANNOVAR lists: GENSCAN lists: PhosphoSiteAnalyzer lists: MethylCoder lists: featureCounts lists: LOCAS lists: Scalpel lists: Cell motility lists: Mouse Genome Database lists: CloudAligner lists: HeurAA lists: GSA-SNP lists: seqMINER lists: PolyPhen: Polymorphism Phenotyping lists: rqubic lists: PlantNATsDB - Plant Natural Antisense Transcripts DataBase lists: MitoBreak lists: Cube-DB lists: Death Domain database lists: Telescoper lists: Crossbow lists: MToolBox lists: GENE-counter lists: BEADS lists: PLAN2L lists: INCLUSive lists: CSAR lists: ApiDB CryptoDB lists: MACS lists: NNcon lists: KAVIAR lists: GeneSigDB lists: psRNATarget lists: Composition Profiler lists: MINAS - Metal Ions in Nucleic AcidS lists: EGSEA lists: Crystallography and NMR System (CNS) lists: Morpheus lists: IUPHAR/BPS Guide to Pharmacology lists: RAST Server lists: ProteomicsDB lists: SPEX2 lists: LTR_Finder lists: SCRATCH lists: DSAP lists: PALEOMIX lists: Buccaneer lists: QuantiSNP lists: ProtTest lists: MultiQC lists: GeneWise lists: DISEASES lists: Off-Spotter lists: oligo lists: 3D-footprint lists: SC3 lists: MS-GF+ lists: TISSUES lists: TFBS lists: CHiCAGO lists: Poretools lists: Membrane Protein Explorer lists: FATCAT lists: Bio-tradis lists: ALTER lists: HISAT2 lists: MetaMapR lists: PhyD3 lists: Exonerate lists: primers4clades lists: Fastml lists: Bamtools lists: Genesis lists: DISULFIND lists: EnrichmentMap lists: LoRDEC lists: mentha lists: IDEPI - IDentify EPItopes lists: Oufti lists: FluxModeCalculator lists: eXpression2Kinases lists: SMAGEXP lists: ProCon - PROteomics CONversion lists: Lifebit Deploit lists: TRANSIT lists: Splicing Express lists: Microscopy Image Browser lists: SARTools lists: SPICE lists: DINIES lists: OmicsNet lists: ngsRelate lists: clusterProfiler lists: NetworkAnalyst lists: FRETBursts lists: Thunder STORM lists: ANOCVA lists: ConsensusClusterPlus lists: CIBERSORT lists: CCTOP lists: scran lists: Rsubread lists: Heatmapper lists: BinPacker lists: Subread lists: UMI-tools lists: Goseq lists: PRSice lists: ScaffMatch lists: EMBOSSMatcher lists: JAMM lists: CentroidFold lists: Gigwa lists: FastProject lists: GeSeq lists: ComplexHeatmap lists: PatchDock lists: Proovread lists: trimAl lists: ExPASy ABCD database lists: shinyGEO lists: AmoebaDB lists: Blood Exposome Database lists: STRUCTURE lists: NetPhos lists: Geneshot lists: ProtParam Tool lists: HiC-Pro lists: HingeProt lists: Mousebytes lists: iTOL lists: ChiCMaxima lists: SWISS-MODEL lists: PASTEClassifier lists: R/qtl2 lists: FlowCal lists: Signaling Pathways Project lists: GPS-SUMO lists: Roary lists: SpydrPick lists: ProSA-web lists: SIGNOR lists: MaxAlign lists: REDIportal lists: EpiModel lists: Protein Interactions Calculator lists: rVista lists: Minimap2 lists: PrognoScan lists: Batch Web CD-Search Tool lists: AlgPred lists: GOnet lists: GalaxyWEB lists: GalaxyRefine lists: Annotree lists: khmer lists: E-CRISP lists: Robetta lists: D-GENIES lists: aroma.light lists: Clustal Omega lists: DESeq lists: VICMpred lists: Ray lists: Apollo lists: STAMP lists: discoSnp lists: vcflib lists: IgBLAST lists: BioPerl lists: Genome BioInformatics Research Lab - gff2ps lists: Rainbow lists: Predictions for Entire Proteomes lists: Stacks lists: Clustal W2 lists: RNAhybrid lists: Primer3 lists: SAMtools/BCFtools lists: EBSeq lists: biobambam lists: DIALIGN lists: Unipro UGENE lists: Bowtie 2 lists: Artemis: Genome Browser and Annotation Tool lists: WHAM lists: Database of Secondary Structure Assignments lists: Minia lists: HTSeq lists: RAxML lists: Sickle lists: Segemehl lists: Staden Package lists: Bismark lists: NCBI BLAST lists: Vienna RNA lists: GBrowse lists: ea-utils lists: AmpliconNoise lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: BitSeq lists: HilbertVis lists: VarScan lists: Regulatory Sequence Analysis Tools lists: CD-HIT lists: MACH lists: SOAPsnp lists: ProbCons lists: BEAST lists: Crux tandem mass spectrometry analysis software lists: Pscan-ChIP lists: BRIG lists: tRNAscan-SE lists: CGView lists: Circos lists: FreeBayes lists: Glimmer lists: T-Coffee lists: Oases lists: LIMMA lists: cutadapt lists: SSAKE lists: edgeR lists: OpenMS lists: Flexbar lists: SIFT lists: Mauve lists: Kalign lists: RSEM lists: TopHat lists: DNAcopy lists: phyloseq lists: Trinity lists: AMOS lists: FastTree lists: Cufflinks lists: Prokka lists: PAML lists: CummeRbund lists: GROMACS lists: minet lists: Atac lists: Pilon lists: GMA lists: Nanopolish lists: Krona lists: SeqPrep lists: SortMeRNA lists: THESIAS lists: tximport lists: StoatyDive lists: rCASC lists: precrec lists: IMGT-ONTOLOGY lists: KAT lists: globaltest lists: COPASI lists: CheckM lists: Blobtools lists: NiftyPET lists: SeaView lists: ASHLAR lists: KisSplice lists: metagen lists: BUSCO lists: BLINK lists: bridge lists: Fcirc lists: becas lists: bwtool lists: TGS-GapCloser lists: chimerascan lists: GLUE lists: mosdepth lists: dcmqi lists: SwiftOrtho lists: andi lists: metahdep lists: HaploReg lists: Jalview lists: ScanITD lists: ImaGene lists: BioNix lists: qrqc lists: MeroX lists: sleuth lists: imDEV lists: MiXCR lists: mlgt lists: SMARTdenovo lists: casper lists: miRDB lists: shovill lists: NiftyFit lists: libmgf lists: rbsurv lists: HH-suite lists: affy lists: StatAlign lists: quantsmooth lists: Fiji lists: yaqcaffy lists: Racon lists: h5vc lists: seqbias lists: tensorflow lists: MGnify lists: ngs.plot lists: dyebias lists: Eoulsan lists: Cuffdiff lists: bsseq lists: VEnCode lists: OrthoFinder lists: genomation lists: SymPy lists: eTRIKS lists: ascat lists: Bridger lists: GADMA lists: lumi lists: PIRATE lists: Hippocampome.org lists: HaTSPiL lists: XL-mHG lists: VETA lists: mitopred lists: ropls lists: sabre lists: scanpy lists: icy lists: plgem lists: MethBase lists: biobakery lists: minfi lists: HyPhy lists: MyGene.info lists: EpiEstim lists: NanoSim lists: fracridge lists: TDimpute lists: Pavian lists: SimVascular lists: qcmetrics lists: Laniakea lists: CRISPRcasIdentifier lists: BISE lists: ODAM lists: MRIcron lists: smashpp lists: BSA4Yeast lists: neuroelectro lists: RepeatFiller lists: ShinyLearner lists: docker4seq lists: CRISPR-ERA lists: MAFFT lists: RepeatScout lists: Phenoscape lists: PhenoMeNal lists: multtest lists: TransDecoder lists: les lists: PlotTwist lists: CRISPR-P lists: Telescope lists: charm lists: Warp lists: skewer lists: Human Neocortical Neurosolver lists: ggtree lists: Datanator lists: genehunter-imprinting lists: GraphClust2 lists: eisa lists: scVelo lists: GEMINI lists: beadarray lists: NGSEP lists: ProP Server lists: CandiMeth lists: METAREP lists: scater lists: BioBERT lists: iontree lists: MetaP lists: larvalign lists: UALCAN lists: VAPPER lists: halSynteny lists: EvidenceFinder lists: bcbio-nextgen lists: QuickNII lists: QIIME lists: phantompeakqualtools lists: MCScan lists: pepwheel lists: PathwayMatcher lists: vsn lists: VisR lists: Galaxy scater lists: OpenWorm lists: ffpe lists: timecourse lists: Metascape lists: Bio2BEL lists: RDXplorer lists: ActiveDriver lists: GENCODE lists: CRISPRdirect lists: GeneMarkS-T lists: SPM lists: Bionitio lists: ascend lists: TCW lists: NanoPipe lists: NeuroChaT lists: pheatmap lists: prank lists: Online Peri-Event Time Histogram for Open Ephys lists: kallisto lists: ggplot2 lists: odMLtables lists: glycomedb lists: pickgene lists: GigaSOM.jl lists: pvac lists: EHRtemporalVariability lists: GemSIM lists: lapmix lists: PAFScaff lists: refgenie lists: biospytial lists: EnteroBase lists: QGIS lists: CLIP-Explorer lists: RatMine lists: NMRProcFlow lists: cn.mops lists: SPP lists: seq-annot lists: PsyGeNET lists: PASA lists: UniCarb-DB lists: NormqPCR lists: PhylomeDB lists: SnpHub lists: ReadqPCR lists: circlize lists: HmtVar lists: sim4cc lists: gprege lists: FusionCatcher lists: UniCarbKB lists: clustergrammer lists: clipcrop lists: metabnorm lists: rnaQUAST lists: VirusMINT lists: breseq lists: PerM lists: SnpEff lists: DecGPU lists: e-Driver lists: NCBI BioProject lists: Flye lists: nondetects lists: PEMer lists: VCFtools lists: STAR lists: fastqz lists: SAMTOOLS lists: Neuroscience Information Framework lists: eProbalign lists: dbEST lists: Dali Server lists: Genomic Ranges lists: GenomicFeatures lists: Cistrome lists: SOAPdenovo lists: IRanges lists: BpForms lists: BcForms lists: DIANA-mirPath lists: AthaMap lists: Ancestrymap lists: AutoDock lists: European Genome phenome Archive lists: GEN3VA lists: 4See lists: ABNER lists: Addgene lists: A Classification of Mobile genetic Elements lists: ADMIXTOOLS lists: AETIONOMY lists: ADMIXMAP lists: ALCHEMY lists: Allele Frequencies in Worldwide Populations lists: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters lists: Alta-Cyclic lists: Alternate splicing gallery lists: Assisted Model Building with Energy Refinement (AMBER) lists: ALOHOMORA lists: AmpliconTagger lists: Molecular Dynamics Workflow (BioKepler) lists: ANDES lists: ALBERT lists: ape lists: ArrayPipe lists: ArrayMiner lists: Aroma.affymetrix lists: ASPEX lists: The Alternatve Splicing Database lists: ASSOCIATIONVIEWER lists: Avogadro lists: AutoAssemblyD lists: BadMedicine lists: BamView lists: BAIT lists: BatMeth lists: AutoDock Vina lists: BARS lists: BCBtoolkit lists: Athena lists: BarraCUDA lists: betaVAEImputation lists: BiG-SLiCE lists: BBSeq lists: SVM based method for predicting beta hairpin structures in proteins lists: BioCarta Pathways lists: BayesEpiModels lists: BiNGO: A Biological Networks Gene Ontology tool lists: BeetleBase lists: BAR lists: BioConda lists: Bioinformatics Toolkit lists: Bionimbus lists: biomaRt lists: Bio++ lists: naiveBayesCall lists: BioSimulations lists: BioPlex lists: Biopieces lists: BRAIN lists: BLAT lists: BS Seeker lists: Breakpointer lists: Canu lists: BioSimulators lists: BRB-ArrayTools lists: bioSyntax lists: CATALYST lists: BOMP: beta-barrel Outer Membrane protein Predictor lists: bioRxiv lists: CAT lists: CCREL lists: BWA lists: CASPAR lists: CARD lists: CATH: Protein Structure Classification lists: CATdb: a Complete Arabidopsis Transcriptome database lists: Cell Image Library (CIL) lists: CEM lists: Cancer Genome Anatomy Project lists: Centrifuge Classifier lists: Bs-Seeker2 lists: ChimeraSlayer lists: ChemSpider lists: BSVF lists: CiLiQuant lists: Chipster lists: CleanEx lists: CHEBI lists: cisTEM lists: CiteFuse lists: clustLasso lists: Chromas lists: ChiRA lists: CNVer lists: CITE-seq-Count lists: CNV-seq lists: circlncRNAnet lists: CMap lists: COGEME Phytopathogenic Fungi and Oomycete EST Database lists: ClinVar lists: ChIPMunk lists: CODEHOP lists: ClustVis lists: CoCo lists: CONTRA lists: Comparative Metatranscriptomics Workflow lists: ComiR lists: CopyDetective lists: ConDeTri lists: Clinotator lists: cortex lists: ClinTrajAn lists: CorMut lists: Coot lists: CRCView lists: CUDASW++ lists: CovalentDock Cloud lists: Chromosome Scale Assembler lists: CYANA lists: Datasets2Tools lists: DBTSS: Database of Transcriptional Start Sites lists: CoryneRegNet lists: CSDeconv lists: CRISPy-web lists: dbSNP lists: ΔG prediction server lists: DGIdb lists: DANPOS2 lists: CorrDrugTumorMSI lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: Dictyostelium discoideum genome database lists: DIAMOND lists: DichroWeb lists: DETONATE lists: DicomTypeTranslator lists: DIME lists: DEXSeq lists: DisProt - Database of Protein Disorder lists: D-EE lists: DAMBE lists: DiffBind lists: DiProGB lists: DOGMA lists: DSK lists: ENIGMA lists: Descriptions of Plant Viruses lists: DOMINE: Database of Protein Interactions lists: Dissect lists: DrivAER lists: Enrichr lists: Variant Effect Predictor lists: EBCall lists: eDMR lists: EMAN lists: Entrez Gene lists: ensembldb lists: Ensembl lists: Epigenomics Workflow on Galaxy and Jupyter lists: Ensembl Genomes lists: epitopepredict lists: DISENTANGLER lists: EpiDISH R package lists: ECLIPSE lists: Experimental Design Assistant lists: EpiGRAPH lists: European Variation Archive (EVA) lists: eQtlBma lists: Eukaryote Genes lists: EXOMEPICKS lists: fineSTRUCTURE lists: Evex lists: Evolutionary Couplings Server lists: Examl lists: NHLBI Exome Sequencing Project (ESP) lists: FlowSOM lists: FireDB lists: FGENESH lists: ExpressYourself lists: fgsea lists: FINDbase Worldwide lists: FateID lists: FluoRender lists: An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application lists: FlexProt: flexible protein alignment lists: FlyBase lists: FLOSS lists: Full-Length cDNA Database lists: FANTOM DB lists: FragGeneScan lists: FuncAssociate: The Gene Set Functionator lists: FastQC lists: Genome Database for Rosaceae lists: Fugu Genome Project lists: FunRich: Functional Enrichment analysis tool lists: GASSST lists: G-Mo.R-Se lists: GeneCodis lists: GASV lists: FusionHunter lists: Genome Annotation Generator lists: GeneSeeker lists: GenePattern Notebook lists: GeCo3 lists: Gene3D lists: GeMoMa lists: GATK lists: Genome Projector lists: Genomedata lists: Gene Expression Atlas lists: GeneProf lists: Genome Trax lists: GENERECON lists: Genometa lists: GEDIT lists: FunCluster lists: Gibbs Motif Sampler lists: GEMB lists: Genome Reviews lists: GensearchNGS lists: GEPAT lists: Genomic Annotation in Livestock for positional candidate LOci lists: Generic GO Term Finder lists: GermOnline lists: VBASE2 lists: GEO2R lists: GFINDer: Genome Function INtegrated Discoverer lists: Generic GO Term Mapper lists: Google lists: Gene Ontology lists: Genome Aggregation Database lists: Gmove lists: Git lists: GNUMAP lists: G protein receptor interaction feature finding instrument lists: Graph2GO lists: Gaggle lists: GoMapMan lists: Gramene lists: GTDB-Tk lists: GO2MSIG lists: GMcloser lists: Genovar lists: Human Gene Mutation Database lists: H-InvDB lists: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology lists: GRASS lists: HTR lists: International HapMap Project lists: HASTE-project lists: HARSH lists: HAPLOCLUSTERS lists: HSSP lists: Homologous Sequences in Ensembl Animal Genomes lists: Human Splicing Finder lists: HPEPDOCK Server lists: HS-TDT lists: HubMed lists: IBIS: Inferred Biomolecular Interactions Server lists: hyfi: software suite for binding site search lists: HiCUP lists: Human Gene Connectome Server lists: Identifiers.org lists: HUGE - Human Unidentified Gene-Encoded large proteins lists: Hybrid-denovo lists: HINT lists: HUDSEN lists: IntEnz- Integrated relational Enzyme database lists: IMG System lists: HCLUST lists: iDASH lists: HiPipe lists: IMGT/StatClonotype lists: I-TASSER lists: IRESite lists: IMEx - The International Molecular Exchange Consortium lists: IMGT/HLA lists: ImJoy lists: IMGT HighV-QUEST lists: IMGT - the international ImMunoGeneTics information system lists: IsoEM lists: IPD - Immuno Polymorphism Database lists: iPiG lists: IPI lists: Isaac lists: Integr8 : Access to complete genomes and proteomes lists: inGAP lists: ISFinder lists: jmzML lists: Interolog/Regulog Database lists: IsoLasso lists: LAST lists: LOCUSMAP lists: J-Express lists: IsaCGH lists: IMG lists: lncRNAdb lists: InterProScan lists: KGGSeq lists: LDSELECT lists: Magic lists: JGI Genome Portal lists: lme4 lists: MAP lists: OntoQuest lists: Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains lists: MACiE lists: LitMiner lists: long-read-tools lists: LOCATE: subcellular localization database lists: LTR_FINDER_parallel lists: Maq lists: MaizeGDB lists: Mammalian Gene Collection lists: Machado lists: LRPath lists: MentaLiST lists: MatrixDB lists: MARRVEL lists: MEBS: Multigenomic Entropy-Based Score lists: Libra lists: LS-SNP/PDB lists: mapDamage lists: Maqview lists: Mascot lists: MAKER lists: MapSplice lists: MetAMOS lists: MethylExtract lists: MBGD - Microbial Genome Database lists: MB-GAN lists: MetaCyc lists: MeQA lists: MEGAHIT lists: Metabolomics Workbench lists: miRBase lists: Metastats lists: MBCluster.Seq lists: metaXplor lists: lsa_slurm lists: MeRIP-PF lists: MendelIHT.jl lists: proMODMatcher lists: mirTools lists: MetaCyto lists: MMAPPR lists: MICSA lists: MIRIAM Resources lists: MaSuRCA lists: UEA sRNA Workbench lists: MetaVelvet lists: miROrtho: the catalogue of animal microRNA genes lists: MERMAID lists: Mspire-Simulator lists: MULTIMAP lists: ML Repo lists: MIP Scaffolder lists: SCIPION lists: MPscan lists: MISA lists: MobiDB lists: MutPred lists: MizBee lists: MRFSEQ lists: MultiLoc lists: MP3 tool lists: Multi-omics Visualization Platform lists: NCBI Probe lists: NeLS lists: MoDIL lists: MPDA lists: Noncoding RNA database lists: Myriads lists: MUMmer lists: Multiple Myeloma survival predictor lists: mrCaNaVaR lists: MULTIDISEQ lists: mzMatch lists: Mouse Phenome Database (MPD) lists: NCBI lists: Ngs backbone lists: NetMHCpan Server lists: miRpathDB lists: NEMBASE lists: Nucleic Acid Database lists: NCBI Genome Workbench lists: NeuroMatic lists: Ngmlr lists: nsSNPAnalyzer lists: Nephele lists: Online Resource for Community Annotation of Eukaryotes lists: Omics Data Paper Generator lists: Necklace lists: NEST Simulator lists: Genotyping lists: NucleoFinder lists: NGSView lists: Open Trials lists: ngLOC lists: NetNGlyc lists: nmrML lists: NURD lists: ObjTables lists: Pathway Tools lists: NeSSM lists: NanoGalaxy lists: PartiGeneDB lists: NOrMAL lists: Open Babel lists: OsiriX Medical Imaging Software lists: PDB Finder lists: Opera lists: Pathbase lists: PEDIGREEQUERY lists: PAZAR lists: PDBe - Protein Data Bank in Europe lists: PanoramaWeb lists: Oncodrive-fm lists: parSMURF lists: Orientations of Proteins in Membranes database lists: PEDHUNTER lists: PeakAnalyzer lists: Illuminating the Druggable Genome lists: Phenotypes and eXposures Toolkit lists: PeakSeq lists: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers lists: PicTar lists: Pash 3.0 lists: Pedigree-Draw lists: OLego lists: Parliament2 lists: Phylogeny.fr lists: PEDPEEL lists: Plant Co-expression Annotation Resource lists: Peakzilla lists: Pfam lists: PhaseME lists: PHI-base lists: Eddy Lab Software lists: PhyML lists: Protein Information Resource lists: PRADA lists: PM4NGS lists: PennSeq lists: Philius lists: PeptideAtlas lists: PHYLIP lists: PhenoMan lists: Proteomics Identifications (PRIDE) lists: pNovo+ lists: ProfCom - Profiling of complex functionality lists: PIRSF lists: PubCrawler lists: PhyloPat lists: PEMA lists: Polygenic Pathways lists: pFind Studio: pLink lists: ProteomeXchange lists: PLANTTFDB lists: PyRosetta lists: Phospho.ELM lists: PRICE lists: PolymiRTS lists: PLINK/SEQ lists: PrimerBank lists: Pyntacle lists: PubChem lists: ProSight Lite lists: PubGene lists: PRED-TMBB lists: Preseq lists: ProtChemSI lists: R Project for Statistical Computing lists: RaptorX lists: QSRA lists: Protein Prospector lists: PrimerSeq lists: R/QTLBIM lists: Reactome lists: PyBEL lists: PS-Plant Framework lists: RepeatModeler lists: QuickGO lists: QmRLFS-finder lists: RefSeq lists: The Human Protein Atlas lists: QGene lists: PolyPhred lists: Rampart lists: ResponseNet lists: QUMA lists: QMSIM lists: RAREMETAL lists: Relate lists: ReactomePA lists: RESID lists: RADAR-base lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: R-SAP lists: Research-tested Intervention Programs (RTIPs) lists: RNA FRABASE - RNA FRAgments search engine and dataBASE lists: Reptile lists: Rdisop lists: RNA-SeQC lists: RNA Virus Database lists: RESCUE-ESE lists: REDItools lists: RegulonDB lists: SeqExpress lists: Scansite lists: RiboTaper lists: SALT lists: riborex lists: REDfly Regulatory Element Database for Drosophilia lists: rna-stability lists: RNAplex lists: rSNP Guide lists: SVA lists: RightField lists: runBioSimulations lists: SAMMate lists: SeqtrimNEXT lists: rSeq lists: SeqEM lists: ROMPREV lists: SeqSaw lists: SHARCGS lists: SAFA Footprinting Software lists: SHELX lists: sapFinder lists: QuPath lists: SIBLINK lists: Seqtk lists: SEEK lists: SMRT View lists: SKAT lists: SimRare lists: SeQuiLa lists: SGA lists: SASQUANT lists: Sherman lists: SilkDB lists: FASTSLINK lists: SASGENE lists: SILVA lists: SGD lists: ShinyGO lists: SimSeq lists: SIDER lists: SMI Services lists: Sniffles lists: STEPS lists: SNP HITLINK lists: SOAPnuke lists: SGN lists: SIBMED lists: SIMULATE lists: rnaSPAdes lists: SpliceMap lists: SMART lists: SnoopCGH lists: SynTView lists: SIMPED lists: Supersplat lists: SnpSift lists: SISSRs lists: Sybil lists: Solas lists: SNPTEST lists: SISYPHUS lists: ASC lists: SOAPfusion lists: TAndem Splice Site DataBase lists: SoupX lists: StSNP lists: T-lex lists: SWEEP lists: SynergyFinder lists: topGO lists: TAPIR: target prediction for plant microRNAs lists: TDT-PC lists: TDR Targets Database lists: SpoTyping lists: ShortFuse lists: SWISS-2DPAGE lists: Spot lists: TAGS lists: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs lists: SUMSTAT lists: TMAJ lists: TASSEL lists: TreeDyn lists: TropGENE DB lists: TB PORTALS lists: SwissTree lists: tradeSeq lists: FLUX CAPACITOR lists: UNAFold lists: Transporter Classification Database lists: ApiDB ToxoDB lists: Trowel lists: TopFIND lists: TRAL lists: Trim Galore lists: Biological General Repository for Interaction Datasets (BioGRID) lists: IQ-TREE lists: VirusSeq lists: Tool recommender system in Galaxy lists: V-Phaser 2 lists: SPIKE lists: Trans-ABySS lists: TRiCoLOR lists: TomoMiner lists: variancePartition lists: TRACESPipe lists: UTRdb/UTRsite lists: UniParc lists: TWOLOC lists: USeq lists: Zebrafish Information Network (ZFIN) lists: XPN lists: TransmiR lists: Webproanalyst lists: UTGB Toolkit lists: VAAST lists: VirusHunter lists: Yeast Search for Transcriptional Regulators And Consensus Tracking lists: zUMIs lists: VaDiR lists: WSsas - Web Service for the SAS tool lists: VFDB - Virulence Factors of Bacterial Pathogens lists: Gene Index Project lists: Vector Alignment Search Tool lists: Vmatch lists: WEIGHTED FDR lists: Xenbase lists: xia2 pipeline lists: YASARA lists: Visualization and Analysis of Networks containing Experimental Data (VANTED) lists: VisSR lists: dbEST lists: DESeq2 lists: DNA DataBank of Japan (DDBJ) lists: FASTX-Toolkit lists: Trimmomatic lists: VIPERdb lists: PhenStat lists: ABySS lists: Integrative Genomics Viewer lists: Human Disease Ontology lists: LINKAGE lists: ConSurf Database lists: Protein Information Resource lists: PredictNLS lists: tRNAscan-SE lists: VeryFastTree lists: RSEM lists: Emboss Water lists: MEtabolomes, TRaits, and INteractions-Knowledge Graph is listed by: Debian is listed by: ELIXIR Tools and Data Services Registry is affiliated with: ELIXIR Tools and Data Services Registry is related to: ms-utils.org is related to: SUP |
Danish Ministry of Higher Education and Science ; European Union Horizon 2020 ELIXIR-EXCELERATE grant 676559 |
DOI:10.1186/s13059-019-1772-6 PMID:26538599 |
Free, Freely available | biotools:bio.tools, r3d100013668 | https://github.com/bio-tools/biotoolsRegistry/, https://bio.tools/bio.tools, https://doi.org/10.17616/R31NJN1G | http://bio.tools | SCR_014695 | 2026-10-17 01:28:49 | 29 | |||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | data access protocol, software resource, web application, web service | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NCI U24 CA159988; NIAAA U01 AA013512; NIAAA U01 AA016662; NIDA P01 DA015027; NIGMS R01 GM088822; NIMH P50 MH078028; NIMH P50 MH096972 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-10-17 01:26:42 | 3155 | ||||
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g:Profiler Resource Report Resource Website 1000+ mentions |
g:Profiler (RRID:SCR_006809) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for functional enrichment analysis and conversions of gene lists. Web based tool for functional profiling of gene lists from large scale experiments. Has web interface with powerful visualization. Used for analyzing data from any organism. | gene, high-throughput, genomics, visualization, statistical analysis, slimmer-type tool, term enrichment, protein interaction, functional similarity, analysis, coexpression, gene id, network enrichment analysis, orthology mapping, genomic locus, ontology or annotation visualization, other analysis, ortholog, functional profile, gene list, ontology, pathway, transcription factor, microrna, regulatory motif, protein-protein interaction, biomolecule, gene expression, gene, homology, single nucleotide polymorphism, dna polymorphism, chromosome, network analysis, disease gene, r |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Ensembl is related to: Ensembl Genomes has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group works with: gProfiler2 |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:21646343 PMID:17478515 PMID:31066453 |
Free, Freely available | OMICS_02223, nif-0000-31975 | SCR_006809 | G:Profiler, g:profiler, gProfiler | 2026-10-17 01:26:42 | 2310 | ||||||
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PhenoM - Phenomics of yeast Mutants Resource Report Resource Website |
PhenoM - Phenomics of yeast Mutants (RRID:SCR_006970) | PhenoM | analysis service resource, data analysis service, data or information resource, database, image collection, production service resource, service resource | Database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae, it allows storing, retrieving, visualizing and data mining the quantitative single-cell measurements extracted from micrographs of the temperature-sensitive (ts) mutant cells. PhenoM allows users to rapidly search and retrieve raw images and their quantified morphological data for genes of interest. The database also provides several data-mining tools, including a PhenoBlast module for phenotypic comparison between mutant strains and a Gene Ontology module for functional enrichment analysis of gene sets showing similar morphological alterations. About one-fifth of the genes in the budding yeast are essential for haploid viability and cannot be functionally assessed using standard genetic approaches such as gene deletion. To facilitate genetic analysis of essential genes, we and others have assembled collections of yeast strains expressing temperature-sensitive (ts) alleles of essential genes. To explore the phenotypes caused by essential gene mutation we used a panel of genetically engineered fluorescent markers to explore the morphology of cells in the ts strain collection using high-throughput microscopy. The database contains quantitative measurements of 1,909,914 cells and 78,194 morphological images for 775 temperature-sensitive mutants spanning 491 different essential genes in permissive temperature (26* C) and restrictive temperature (32* C). The morphological images were generated by high-content screening (HCS) technology. | phenomics, phenotype, yeast, mutant, cell, morphology, essential gene, gene, high-content screening, microscopy, micrograph, mutant cell, temperature-sensitive allele, allele, genetic analysis, blast, mutation, orf, actin, dna damage, nucleus, mitochondria, plasma membrane, mitotic spindle, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Research Fund ; Fudan University - University of Toronto Exchange Scholarship ; Canadian Institutes of Health Research GMX-201237; Canadian Institutes of Health Research GMX-211012; Canadian Foundation for Innovation LEF-21475 |
PMID:22009677 | Free | nlx_151489, biotools:phenom, r3d100012722 | https://bio.tools/phenom, https://doi.org/10.17616/R3GJ5J | SCR_006970 | Phenomics of yeast Mutants, Phenomics of yeast Mutants (PhenoM) | 2026-10-17 01:26:46 | 0 | ||||
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FunNet - Transcriptional Networks Analysis Resource Report Resource Website 10+ mentions |
FunNet - Transcriptional Networks Analysis (RRID:SCR_006968) | FunNet | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | Functional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genome, transcriptional interaction, microarray, gene expression, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: KEGG has parent organization: Cordelier Research Center |
PMID:18208606 | Free for academic use, GNU General Public License, v2 | nlx_149243 | SCR_006968 | Functional Analysis of Transcriptional Networks, Functional Analysis of Transcriptional Networks (FunNet) | 2026-10-17 01:26:48 | 17 | ||||||
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GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-10-17 01:26:45 | 6 | |||||
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agriGO Resource Report Resource Website 1000+ mentions |
agriGO (RRID:SCR_006989) | agriGO | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | browser, gene, online tool, visualization, statistical analysis, term enrichment, text mining, ontology or annotation browser, ontology or annotation visualization, database or data warehouse, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: China Agricultural University; Beijing; China |
Ministry of Science and Technology of China 90817006; Ministry of Science and Technology of China 2006CB100105 |
PMID:20435677 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149099, OMICS_02265, biotools:agrigo | https://bio.tools/agrigo | SCR_006989 | agriGO -- GO Analysis Toolkit and Database for Agricultural Community | 2026-10-17 01:26:45 | 1743 | ||||
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YeTFaSCo Resource Report Resource Website 10+ mentions |
YeTFaSCo (RRID:SCR_006893) | YeTFaSCo | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome. | transcription factor, binding site, sequence, yeast, motif, gene, genome, protein, protein complex |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Graduate Scholarship awards ; Canadian Institutes of Health Research Operating Grant MOP-490425; Canadian Institutes of Health Research Operating Grant MOP-86705 |
PMID:22102575 | Acknowledgement requested | nlx_151611, OMICS_01861 | SCR_006893 | Yeast Transcription Factor Specificity Compendium, YeTFaSCo: The Yeast Transcription Factor Specificity Compendium | 2026-10-17 01:26:44 | 34 | |||||
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DynGO Resource Report Resource Website 1+ mentions |
DynGO (RRID:SCR_007009) | DynGO | software resource | DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Requirements: Java Platform: Windows compatible, Linux compatible, Unix compatible | gene, annotation, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
NSF IIS-0430743 | PMID:16091147 | Free for academic use | nlx_149118 | http://gauss.dbb.georgetown.edu/liblab | SCR_007009 | DynGO: a tool for visualizing and mining of Gene Ontology and its associations | 2026-10-17 01:26:46 | 6 | ||||
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OBO Resource Report Resource Website 100+ mentions |
OBO (RRID:SCR_007083) | OBO | controlled vocabulary, data or information resource, knowledge environment, narrative resource, ontology, standard specification | A collaboration involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. In addition to a listing of OBO ontologies, this site provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development. Feedback is welcome and participation encouraged. | biomedical, metadata standard, gold standard, FASEB list |
lists: CHEBI lists: NCI Thesaurus lists: Porifera Ontology lists: Gazetteer lists: Human Disease Ontology lists: Information Artifact Ontology lists: Teleost Anatomy Ontology lists: Gene Ontology lists: Spider Ontology lists: Mental Functioning Ontology lists: Ascomycete Phenotype Ontology lists: Beta Cell Genomics Ontology lists: Biological Collections Ontology lists: Emotion Ontology lists: Chemical Methods Ontology lists: Chemical Information Ontology lists: Clinical Measurement Ontology lists: Common Anatomy Reference Ontology lists: Experimental Conditions Ontology lists: Dictyostelium Discoideum Anatomy Ontology lists: Fission Yeast Phenotype Ontology lists: Fly Taxonomy lists: FlyBase Controlled Vocabulary lists: Hymenoptera Anatomy Ontology lists: Influenza Ontology lists: Lipid Ontology lists: Kinetic Simulation Algorithm Ontology lists: Malaria Ontology lists: Measurement Method Ontology lists: Minimal Anatomical Terminology lists: Ontology for Genetic Interval lists: Ontology for Parasite LifeCycle lists: Ontology of Adverse Events lists: Ontology of Medically Related Social Entities lists: Ontology of Vaccine Adverse Events lists: Rat Strain Ontology lists: Plant Environmental Conditions lists: Plant Trait Ontology lists: Population and Community Ontology lists: RNA Ontology lists: Rat Strain Ontology lists: Subcellular Anatomy Ontology lists: Software Ontology lists: Suggested Ontology for Pharmacogenomics lists: Vertebrate Taxonomy Ontology lists: Physico-Chemical Process lists: Adverse Event Reporting Ontology lists: Xenopus Anatomy Ontology lists: Cell Line Ontology lists: Human Phenotype Ontology lists: Neurobehavior Ontology lists: Ontology for Biomedical Investigations lists: Comparative Data Analysis Ontology lists: Ontology for General Medical Science lists: Physico-Chemical Methods and Properties lists: Gene Regulation Ontology is listed by: FORCE11 is related to: MeGO is related to: Drosophila anatomy and development ontologies is related to: Cell Type Ontology is related to: OBO-Edit is related to: go-perl is related to: OWLTools is related to: Zebrafish Anatomical Ontology is related to: OBO Tracker: Plant Ontology (PO) TERM requests is related to: eVOC is related to: OnEx - Ontology Evolution Explorer is related to: BioPerl is related to: dkCOIN is related to: Standards-based Infrastructure with Distributed Resources is related to: OntoVisT is related to: COBrA is related to: Wandora is related to: ONTO-PERL is related to: Genomic Standards Consortium is related to: Ontology Lookup Service is related to: LexGrid is related to: SBO is related to: RIKEN integrated database of mammals is related to: DOAF is related to: Gene Ontology is related to: African Population Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects is parent organization of: OBO Relation Ontology is parent organization of: SO is parent organization of: PATO is parent organization of: MPO is parent organization of: AEO is parent organization of: UBERON |
PMID:17989687 | nlx_22892 | SCR_007083 | The Open Biomedical Ontologies, OBO Foundry, Open Biological and Biomedical Ontologies, Open Biological and Biomedical Ontology Foundry | 2026-10-17 01:26:48 | 182 | |||||||
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EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | data analysis software, data processing software, software application, software resource | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-10-17 01:27:19 | 8 | |||||
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Tk-GO Resource Report Resource Website |
Tk-GO (RRID:SCR_008855) | TkGO | software resource | Tk-GO is a GUI wrapping the basic functions of the GO AppHandle library from BDGP. GO terms are presented in an explorer-like browser, and behavior can be configured by altering Perl scripts. All available documentation is included in the download. Tk-GO uses the GO database (connects directly to the BDGP database by default) but is user-configurable. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | browser, gene, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Illumina |
MIT License - Free for academic use | nlx_149133 | SCR_008855 | 2026-10-17 01:27:12 | 0 | ||||||||
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Spotfire Resource Report Resource Website 100+ mentions |
Spotfire (RRID:SCR_008858) | Spotfire | software resource | The Spotfire Gene Ontology Advantage Application integrates GO annotations with gene expression analysis in Spotfire DecisionSite for Functional Genomics. Researchers can select a subset of genes in DecisionSite visualizations and display their distribution in the Gene Ontology hierarchy. Similarly, selection of any process, function or cellular location in the Gene Ontology hierarchy automatically marks the corresponding genes in DecisionSite visualizations. Platform: Windows compatible | analysis, predictive analytics, big data, visualization, gene ontology, annotation, gene expression, functional genomics, gene, function, cellular location, statistical analysis, genomics |
is listed by: Gene Ontology Tools is listed by: Metabolomics Workbench is related to: Gene Ontology |
Commercial license. Spotfire is available for purchase (individual license / enterprise use) / Free trial. | nlx_149169 | SCR_008858 | Tibco Spotfire, Spotfire Inc., Spotfire Gene Ontology Advantage Application, Spotfire - TIBCO Software | 2026-10-17 01:27:32 | 490 | |||||||
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Gene Ontology Extension Resource Report Resource Website |
Gene Ontology Extension (RRID:SCR_010327) | GO-EXT | controlled vocabulary, data or information resource, ontology | An extension of the Gene Ontology. | obo |
is listed by: BioPortal has parent organization: Gene Ontology |
nlx_157414 | SCR_010327 | 2026-10-17 01:27:33 | 0 | |||||||||
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AgingDB Resource Report Resource Website |
AgingDB (RRID:SCR_010226) | AgingDB | data or information resource, data repository, database, service resource, storage service resource | A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments. | oxidative stress, calorie restriction, pathway, biomolecule, signal pathway, interaction, gene, protein, protein-protein interaction, apoptosis, mitochondrial, nuclear transcription factor |
is related to: Gene Ontology has parent organization: Pusan National University; Busan; South Korea |
Aging | PMID:23604914 | The community can contribute to this resource | nlx_156773 | http://aging.pharm.pusan.ac.kr/AgingDB/ | SCR_010226 | Aging Database, Aging DB | 2026-10-17 01:27:15 | 0 | ||||
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MitoMiner Resource Report Resource Website 50+ mentions |
MitoMiner (RRID:SCR_001368) | data or information resource, database | A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java. | mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, ortholog, FASEB list |
uses: HomoloGene uses: UniProt uses: KEGG uses: OMIM uses: The Human Protein Atlas uses: Gene Ontology |
MRC | PMID:22121219 PMID:19208617 |
Public, Acknowledgement requested, Code: | nlx_152504 | SCR_001368 | MitoMiner - A database of the mitochondrial proteome | 2026-10-17 01:32:57 | 78 |
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