FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

scientific article (publication date: March 2004)

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes is …
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scholarly articleQ13442814

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P8978DBLP publication IDjournals/bioinformatics/Al-ShahrourDD04
P356DOI10.1093/BIOINFORMATICS/BTG455
P3181OpenCitations bibliographic resource ID37253
P698PubMed publication ID14990455
P5875ResearchGate publication ID8682332

P2093author name stringDopazo J
Díaz-Uriarte R
Al-Shahrour F
P433issue4
P407language of work or nameEnglishQ1860
P921main subjectontologyQ324254
Gene OntologyQ135085
P304page(s)578-80
P577publication date2004-03-01
P1433published inBioinformaticsQ4914910
P1476titleFatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
P478volume20

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Q30482057M-BISON: microarray-based integration of data sources using networks
Q33321682MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters
Q97418793MMiRNA-Viewer2, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network
Q37091537Macrophage responses to silica nanoparticles are highly conserved across particle sizes
Q35829278Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations
Q34993600Maternal nutrition induces gene expression changes in fetal muscle and adipose tissues in sheep
Q35129397MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Q35921899Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis
Q36009771Metabolic Context of the Competence-Induced Checkpoint for Cell Replication in Streptococcus suis
Q38498163Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership
Q31058333Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes
Q36945167MicroRNA-directed transcriptional gene silencing in mammalian cells
Q34099564Microarray analyses of gene expression during chondrocyte differentiation identifies novel regulators of hypertrophy
Q81516058Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy
Q33236607Microarray based comparison of two Escherichia coli O157:H7 lineages
Q53226601Modulation in proteolytic activity is identified as a hallmark of exogen by transcriptional profiling of hair follicles.
Q38435630Molecular Evidence for Differential Long-term Outcomes of Early Life Severe Acute Malnutrition.
Q33484497Molecular characterization of hybridoma subclones spontaneously switching at high frequencies in vitro
Q33288114Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera
Q34120522Molecular evidence for arterial repair in atherosclerosis
Q64041498Molecular evidence of field cancerization initiated by diabetes in colon cancer patients
Q33455595Molecular signatures of prostate stem cells reveal novel signaling pathways and provide insights into prostate cancer
Q34192750Multi-objective differential evolution for automatic clustering with application to micro-array data analysis
Q30494248Multidimensional gene set analysis of genomic data
Q36168447Multidimensional protein identification technology: current status and future prospects
Q35448459Murine candidate bleomycin induced pulmonary fibrosis susceptibility genes identified by gene expression and sequence analysis of linkage regions
Q51854544Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT-PCR tools.
Q39630080Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs
Q35879358Mycobacterial bacilli are metabolically active during chronic tuberculosis in murine lungs: insights from genome-wide transcriptional profiling
Q38502454NOA: a novel Network Ontology Analysis method
Q30939961New challenges in gene expression data analysis and the extended GEPAS
Q31048894Next station in microarray data analysis: GEPAS.
Q36161269Nitric oxide participates in plant flowering repression by ascorbate
Q36615425No common denominator for breast cancer lymph node metastasis
Q21245331Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay
Q30544655Novel Foxo1-dependent transcriptional programs control T(reg) cell function
Q37548517Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
Q34011529Null mutations in human and mouse orthologs frequently result in different phenotypes
Q33777394Obesity related methylation changes in DNA of peripheral blood leukocytes
Q33675232Oncogenes and pathway identification using filter-based approaches between various carcinoma types in lung
Q36925400One-hit effects in cancer: altered proteome of morphologically normal colon crypts in familial adenomatous polyposis
Q33954273OntoVisT: A general purpose Ontological Visualization Tool
Q33484932Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila
Q30993399Ontological analysis of gene expression data: current tools, limitations, and open problems
Q30002309Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery
Q27313535Ontology engineering
Q38521681OntologyTraverser: an R package for GO analysis.
Q90329848Oregano essential oil vapour prevents Plasmopara viticola infection in grapevine (Vitis Vinifera) and primes plant immunity mechanisms
Q36007397Oxidative stress, gene expression, and protein changes induced in the human placenta during labor
Q36008487PAGER: constructing PAGs and new PAG-PAG relationships for network biology
Q37189947PGC-1alpha and ERRalpha target gene downregulation is a signature of the failing human heart
Q36787398PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes
Q30846922PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data
Q40617973PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation
Q36749398PaLS: filtering common literature, biological terms and pathway information
Q37096010Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction
Q31116638PathExpress: a web-based tool to identify relevant pathways in gene expression data
Q38165872Pathophysiology of tobacco smoke exposure: recent insights from comparative and redox proteomics
Q38926829Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett's Esophagus Patients
Q41688254Pathway Interaction Network Analysis Identifies Dysregulated Pathways in Human Monocytes Infected by Listeria monocytogenes.
Q37364514Pathway analyses and understanding disease associations
Q33887660Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
Q31067183Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways
Q59791435Pathways and Network Based Analysis of Candidate Genes to Reveal Cross-Talk and Specificity in the Sorghum ( (L.) Moench) Responses to Drought and It's Co-occurring Stresses
Q28255878Pathways to the analysis of microarray data
Q37202538PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
Q35039436PhyloPat: phylogenetic pattern analysis of eukaryotic genes
Q49357708Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events.
Q33242801Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome
Q38375823Predicting novel human gene ontology annotations using semantic analysis
Q21184170Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart
Q42021181Principles of transcriptional regulation and evolution of the metabolic system in E. coli
Q31154589ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
Q51009753Profiling and semiquantitative analysis of the cell surface proteome in human mesenchymal stem cells.
Q34582072Profiling of the embryonic Atlantic halibut (Hippoglossus hippoglossus L.) transcriptome reveals maternal transcripts as potential markers of embryo quality
Q21263197Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex
Q41237074Programmed cell death activated by Rose Bengal in Arabidopsis thaliana cell suspension cultures requires functional chloroplasts.
Q39559618Prolyl endopeptidase is involved in cellular signalling in human neuroblastoma SH-SY5Y cells
Q30956882ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses.
Q37324394Protease gene duplication and proteolytic activity in Drosophila female reproductive tracts
Q37002789Protein expression in a Drosophila model of Parkinson's disease
Q30531062Protein kinase C mediated extraembryonic endoderm differentiation of human embryonic stem cells
Q45929720Protein nitration during defense response in Arabidopsis thaliana.
Q28477611Proteomic analysis of excretory-secretory products of Heligmosomoides polygyrus assessed with next-generation sequencing transcriptomic information
Q36884872Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions
Q36696387Public databases and software for the pathway analysis of cancer genomes.
Q35557599PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level.
Q35914539Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production
Q33835688Quantitative mass spectrometry-based proteomics reveals the dynamic range of primary mouse astrocyte protein secretion
Q92538759Rainbow Trout IgM+ B Cells Preferentially Respond to Thymus-Independent Antigens but Are Activated by CD40L
Q35012892Ranked prediction of p53 targets using hidden variable dynamic modeling
Q24813244Recent additions and improvements to the Onto-Tools
Q58805459Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method
Q35620910Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes.
Q42183551Regulation of Cellular Metabolism and Cytokines by the Medicinal Herb Feverfew in the Human Monocytic THP-1 Cells
Q33527391Regulation of gene expression by PI3K in mouse growth plate chondrocytes
Q35616354Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci.
Q34382690Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes
Q38453642Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard
Q33695755Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology
Q38501548RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology.
Q33372132SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency
Q37245782SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks
Q35537135SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms
Q33719497Selection upon genome architecture: conservation of functional neighborhoods with changing genes
Q57639818Senescence-associated ribosome biogenesis defects contributes to cell cycle arrest through the Rb pathway
Q83223962Sequential gene expression changes in cancer cell lines after treatment with the demethylation agent 5-Aza-2'-deoxycytidine
Q33210921Side population cells isolated from different tissues share transcriptome signatures and express tissue-specific markers.
Q38521075Significance analysis of functional categories in gene expression studies: a structured permutation approach
Q33633483Similarly strong purifying selection acts on human disease genes of all evolutionary ages
Q98184282Single berry reconstitution prior to RNA-sequencing reveals novel insights into transcriptomic remodeling by leafroll virus infections in grapevines
Q90291374Social environment affects the transcriptomic response to bacteria in ant queens
Q33904678Solar ultraviolet radiation is necessary to enhance grapevine fruit ripening transcriptional and phenolic responses
Q38457953Splenic gene expression profiling in White Leghorn layer inoculated with the Salmonella enterica serovar Enteritidis.
Q35588741Stage-specific signaling pathways during murine testis development and spermatogenesis: A pathway-based analysis to quantify developmental dynamics.
Q34165669Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation.
Q27860739Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Q34772247Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development
Q31087210Systematic interpretation of microarray data using experiment annotations
Q84543239Systemic response to Campylobacter jejuni infection by profiling gene transcription in the spleens of two genetic lines of chickens
Q33904892TAFFEL: Independent Enrichment Analysis of gene sets
Q42367962TET2- and TDG-mediated changes are required for the acquisition of distinct histone modifications in divergent terminal differentiation of myeloid cells.
Q90557927Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a 'sweet' crop with 'bitter' genomes
Q36083151Temperature desynchronizes sugar and organic acid metabolism in ripening grapevine fruits and remodels their transcriptome
Q29615564Ten years of pathway analysis: current approaches and outstanding challenges
Q33365805Testing gene set enrichment for subset of genes: Sub-GSE.
Q28249847Text mining for metabolic pathways, signaling cascades, and protein networks
Q38510213Text-based over-representation analysis of microarray gene lists with annotation bias
Q21184158Text-mining and information-retrieval services for molecular biology
Q38510620Text-mining approach to evaluate terms for ontology development
Q30362316The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
Q33529113The Arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes.
Q24643720The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
Q35926110The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations
Q33325831The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site
Q58799510The blind men and the elephant: on meeting the problem of multiple truths in data from clustering and pattern mining perspectives
Q33913372The common ground of genomics and systems biology
Q47407077The consequence of natural selection on genetic variation in the mouse
Q36435183The corepressor NCoR1 antagonizes PGC-1α and estrogen-related receptor α in the regulation of skeletal muscle function and oxidative metabolism
Q33687003The distribution of GYR- and YLP-like motifs in Drosophila suggests a general role in cuticle assembly and other protein-protein interactions
Q39688765The effects of two different ganoderma species (Lingzhi) on gene expression in human monocytic THP-1 cells
Q33695101The evolutionary young miR-1290 favors mitotic exit and differentiation of human neural progenitors through altering the cell cycle proteins.
Q57167930The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus
Q33939198The implications of relationships between human diseases and metabolic subpathways
Q34306294The limitations of simple gene set enrichment analysis assuming gene independence
Q57286200The modular network structure of the mutational landscape of Acute Myeloid Leukemia
Q97517328The morbid cutaneous anatomy of the human genome revealed by a bioinformatic approach
Q36561944The peroxisome proliferator-activated receptor γ coactivator 1α/β (PGC-1) coactivators repress the transcriptional activity of NF-κB in skeletal muscle cells
Q34987266The role of the interactome in the maintenance of deleterious variability in human populations
Q24798755The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome
Q33909410Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization
Q33957849ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems
Q34181781Toward a complete in silico, multi-layered embryonic stem cell regulatory network
Q24811476Towards precise classification of cancers based on robust gene functional expression profiles
Q51248525Toxicogenomics in Environmental Science.
Q55351697Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease.
Q33240474Transcription profiles of non-immortalized breast cancer cell lines
Q34056556Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program
Q34195101Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development
Q90752922Transcriptome Characterization of Reverse Development in Turritopsis dohrnii (Hydrozoa, Cnidaria)
Q36740212Transcriptome Response Mediated by Cold Stress in Lotus japonicus
Q35126175Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions
Q35560029Transcriptome and metabolome reprogramming in Vitis vinifera cv. Trincadeira berries upon infection with Botrytis cinerea
Q93067758Transcriptome assembly and annotation of johnsongrass (Sorghum halepense) rhizomes identify candidate rhizome-specific genes
Q44809252Transcriptome-wide identification of RNA binding sites by CLIP-seq
Q36054045Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection
Q42618762Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage.
Q33456236Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set.
Q31043070Transforming omics data into context: bioinformatics on genomics and proteomics raw data
Q34422921Understanding disease mechanisms with models of signaling pathway activities.
Q35940326Unravelling molecular responses to moderate dehydration in harvested fruit of sweet orange (Citrus sinensis L. Osbeck) using a fruit-specific ABA-deficient mutant
Q33483794Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria
Q33543998Use of microarray technology to assess the time course of liver stress response after confinement exposure in gilthead sea bream (Sparus aurata L.).
Q50315637Using predictive specificity to determine when gene set analysis is biologically meaningful
Q37455170Utility of mass spectrometry for proteome analysis: part II. Ion-activation methods, statistics, bioinformatics and annotation
Q33402870Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements.
Q34550067Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis
Q45905497VirtualPlant: a software platform to support systems biology research.
Q24801533Visualization and analysis of microarray and gene ontology data with treemaps
Q33984285Visualizing information across multidimensional post-genomic structured and textual databases
Q33800456Vorinostat interferes with the signaling transduction pathway of T-cell receptor and synergizes with phosphoinositide-3 kinase inhibitors in cutaneous T-cell lymphoma.
Q36954017WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013
Q36051062Web-based network analysis and visualization using CellMaps
Q33239646Whitefly (Bemisia tabaci) genome project: analysis of sequenced clones from egg, instar, and adult (viruliferous and non-viruliferous) cDNA libraries
Q38333915Whole blood genome-wide expression profiling and network analysis suggest MELAS master regulators
Q31096199Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana
Q64088316Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Uncovers Its Hybrid Origin
Q38373934agriGO: a GO analysis toolkit for the agricultural community
Q38296436cDNA microarray analysis of differentially expressed genes in penile tissue after treatment with tadalafil.
Q38302104g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments
Q24301438hCLE/CGI-99, a human protein that interacts with the influenza virus polymerase, is a mRNA transcription modulator

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