scholarly article | Q13442814 |
P8978 | DBLP publication ID | journals/bioinformatics/Al-ShahrourDD04 |
P356 | DOI | 10.1093/BIOINFORMATICS/BTG455 |
P3181 | OpenCitations bibliographic resource ID | 37253 |
P698 | PubMed publication ID | 14990455 |
P5875 | ResearchGate publication ID | 8682332 |
P2093 | author name string | Dopazo J | |
Díaz-Uriarte R | |||
Al-Shahrour F | |||
P433 | issue | 4 | |
P407 | language of work or name | English | Q1860 |
P921 | main subject | ontology | Q324254 |
Gene Ontology | Q135085 | ||
P304 | page(s) | 578-80 | |
P577 | publication date | 2004-03-01 | |
P1433 | published in | Bioinformatics | Q4914910 |
P1476 | title | FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes | |
P478 | volume | 20 |
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Q45210539 | Integrative systems analysis of diet-induced obesity identified a critical transition in the transcriptomes of the murine liver and epididymal white adipose tissue |
Q36580905 | Interpreting experimental results using gene ontologies |
Q34472537 | Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake. |
Q46158700 | Intrahost Genetic Diversity of Bacterial Symbionts Exhibits Evidence of Mixed Infections and Recombinant Haplotypes |
Q37538175 | Investigating the different mechanisms of genotoxic and non-genotoxic carcinogens by a gene set analysis |
Q33801632 | Investigating the effect of paralogs on microarray gene-set analysis |
Q35097603 | Is transcriptomic regulation of berry development more important at night than during the day? |
Q31048901 | JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information |
Q35075729 | KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases |
Q34974449 | KOBAS server: a web-based platform for automated annotation and pathway identification |
Q33860855 | LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures |
Q33848195 | LYN is a mediator of epithelial-mesenchymal transition and a target of dasatinib in breast cancer |
Q40380499 | Laboratory variability does not preclude identification of biological functions impacted by hydroxyurea |
Q24817221 | Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains |
Q34445068 | Learning dysregulated pathways in cancers from differential variability analysis |
Q36274605 | Linking microarray reporters with protein functions |
Q80130796 | Linking oncogenic pathways with therapeutic opportunities |
Q33287976 | LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs |
Q30482057 | M-BISON: microarray-based integration of data sources using networks |
Q33321682 | MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters |
Q97418793 | MMiRNA-Viewer2, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network |
Q37091537 | Macrophage responses to silica nanoparticles are highly conserved across particle sizes |
Q35829278 | Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations |
Q34993600 | Maternal nutrition induces gene expression changes in fetal muscle and adipose tissues in sheep |
Q35129397 | MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis |
Q35921899 | Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis |
Q36009771 | Metabolic Context of the Competence-Induced Checkpoint for Cell Replication in Streptococcus suis |
Q38498163 | Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership |
Q31058333 | Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes |
Q36945167 | MicroRNA-directed transcriptional gene silencing in mammalian cells |
Q34099564 | Microarray analyses of gene expression during chondrocyte differentiation identifies novel regulators of hypertrophy |
Q81516058 | Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy |
Q33236607 | Microarray based comparison of two Escherichia coli O157:H7 lineages |
Q53226601 | Modulation in proteolytic activity is identified as a hallmark of exogen by transcriptional profiling of hair follicles. |
Q38435630 | Molecular Evidence for Differential Long-term Outcomes of Early Life Severe Acute Malnutrition. |
Q33484497 | Molecular characterization of hybridoma subclones spontaneously switching at high frequencies in vitro |
Q33288114 | Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera |
Q34120522 | Molecular evidence for arterial repair in atherosclerosis |
Q64041498 | Molecular evidence of field cancerization initiated by diabetes in colon cancer patients |
Q33455595 | Molecular signatures of prostate stem cells reveal novel signaling pathways and provide insights into prostate cancer |
Q34192750 | Multi-objective differential evolution for automatic clustering with application to micro-array data analysis |
Q30494248 | Multidimensional gene set analysis of genomic data |
Q36168447 | Multidimensional protein identification technology: current status and future prospects |
Q35448459 | Murine candidate bleomycin induced pulmonary fibrosis susceptibility genes identified by gene expression and sequence analysis of linkage regions |
Q51854544 | Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT-PCR tools. |
Q39630080 | Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs |
Q35879358 | Mycobacterial bacilli are metabolically active during chronic tuberculosis in murine lungs: insights from genome-wide transcriptional profiling |
Q38502454 | NOA: a novel Network Ontology Analysis method |
Q30939961 | New challenges in gene expression data analysis and the extended GEPAS |
Q31048894 | Next station in microarray data analysis: GEPAS. |
Q36161269 | Nitric oxide participates in plant flowering repression by ascorbate |
Q36615425 | No common denominator for breast cancer lymph node metastasis |
Q21245331 | Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay |
Q30544655 | Novel Foxo1-dependent transcriptional programs control T(reg) cell function |
Q37548517 | Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans |
Q34011529 | Null mutations in human and mouse orthologs frequently result in different phenotypes |
Q33777394 | Obesity related methylation changes in DNA of peripheral blood leukocytes |
Q33675232 | Oncogenes and pathway identification using filter-based approaches between various carcinoma types in lung |
Q36925400 | One-hit effects in cancer: altered proteome of morphologically normal colon crypts in familial adenomatous polyposis |
Q33954273 | OntoVisT: A general purpose Ontological Visualization Tool |
Q33484932 | Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila |
Q30993399 | Ontological analysis of gene expression data: current tools, limitations, and open problems |
Q30002309 | Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery |
Q27313535 | Ontology engineering |
Q38521681 | OntologyTraverser: an R package for GO analysis. |
Q90329848 | Oregano essential oil vapour prevents Plasmopara viticola infection in grapevine (Vitis Vinifera) and primes plant immunity mechanisms |
Q36007397 | Oxidative stress, gene expression, and protein changes induced in the human placenta during labor |
Q36008487 | PAGER: constructing PAGs and new PAG-PAG relationships for network biology |
Q37189947 | PGC-1alpha and ERRalpha target gene downregulation is a signature of the failing human heart |
Q36787398 | PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes |
Q30846922 | PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data |
Q40617973 | PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation |
Q36749398 | PaLS: filtering common literature, biological terms and pathway information |
Q37096010 | Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction |
Q31116638 | PathExpress: a web-based tool to identify relevant pathways in gene expression data |
Q38165872 | Pathophysiology of tobacco smoke exposure: recent insights from comparative and redox proteomics |
Q38926829 | Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett's Esophagus Patients |
Q41688254 | Pathway Interaction Network Analysis Identifies Dysregulated Pathways in Human Monocytes Infected by Listeria monocytogenes. |
Q37364514 | Pathway analyses and understanding disease associations |
Q33887660 | Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps |
Q31067183 | Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways |
Q59791435 | Pathways 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 |
Q28255878 | Pathways to the analysis of microarray data |
Q37202538 | PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood |
Q35039436 | PhyloPat: phylogenetic pattern analysis of eukaryotic genes |
Q49357708 | Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events. |
Q33242801 | Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome |
Q38375823 | Predicting novel human gene ontology annotations using semantic analysis |
Q21184170 | Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart |
Q42021181 | Principles of transcriptional regulation and evolution of the metabolic system in E. coli |
Q31154589 | ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data |
Q51009753 | Profiling and semiquantitative analysis of the cell surface proteome in human mesenchymal stem cells. |
Q34582072 | Profiling of the embryonic Atlantic halibut (Hippoglossus hippoglossus L.) transcriptome reveals maternal transcripts as potential markers of embryo quality |
Q21263197 | Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex |
Q41237074 | Programmed cell death activated by Rose Bengal in Arabidopsis thaliana cell suspension cultures requires functional chloroplasts. |
Q39559618 | Prolyl endopeptidase is involved in cellular signalling in human neuroblastoma SH-SY5Y cells |
Q30956882 | ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses. |
Q37324394 | Protease gene duplication and proteolytic activity in Drosophila female reproductive tracts |
Q37002789 | Protein expression in a Drosophila model of Parkinson's disease |
Q30531062 | Protein kinase C mediated extraembryonic endoderm differentiation of human embryonic stem cells |
Q45929720 | Protein nitration during defense response in Arabidopsis thaliana. |
Q28477611 | Proteomic analysis of excretory-secretory products of Heligmosomoides polygyrus assessed with next-generation sequencing transcriptomic information |
Q36884872 | Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions |
Q36696387 | Public databases and software for the pathway analysis of cancer genomes. |
Q35557599 | PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. |
Q35914539 | Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production |
Q33835688 | Quantitative mass spectrometry-based proteomics reveals the dynamic range of primary mouse astrocyte protein secretion |
Q92538759 | Rainbow Trout IgM+ B Cells Preferentially Respond to Thymus-Independent Antigens but Are Activated by CD40L |
Q35012892 | Ranked prediction of p53 targets using hidden variable dynamic modeling |
Q24813244 | Recent additions and improvements to the Onto-Tools |
Q58805459 | Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method |
Q35620910 | Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes. |
Q42183551 | Regulation of Cellular Metabolism and Cytokines by the Medicinal Herb Feverfew in the Human Monocytic THP-1 Cells |
Q33527391 | Regulation of gene expression by PI3K in mouse growth plate chondrocytes |
Q35616354 | Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. |
Q34382690 | Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes |
Q38453642 | Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard |
Q33695755 | Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology |
Q38501548 | RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology. |
Q33372132 | SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency |
Q37245782 | SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks |
Q35537135 | SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms |
Q33719497 | Selection upon genome architecture: conservation of functional neighborhoods with changing genes |
Q57639818 | Senescence-associated ribosome biogenesis defects contributes to cell cycle arrest through the Rb pathway |
Q83223962 | Sequential gene expression changes in cancer cell lines after treatment with the demethylation agent 5-Aza-2'-deoxycytidine |
Q33210921 | Side population cells isolated from different tissues share transcriptome signatures and express tissue-specific markers. |
Q38521075 | Significance analysis of functional categories in gene expression studies: a structured permutation approach |
Q33633483 | Similarly strong purifying selection acts on human disease genes of all evolutionary ages |
Q98184282 | Single berry reconstitution prior to RNA-sequencing reveals novel insights into transcriptomic remodeling by leafroll virus infections in grapevines |
Q90291374 | Social environment affects the transcriptomic response to bacteria in ant queens |
Q33904678 | Solar ultraviolet radiation is necessary to enhance grapevine fruit ripening transcriptional and phenolic responses |
Q38457953 | Splenic gene expression profiling in White Leghorn layer inoculated with the Salmonella enterica serovar Enteritidis. |
Q35588741 | Stage-specific signaling pathways during murine testis development and spermatogenesis: A pathway-based analysis to quantify developmental dynamics. |
Q34165669 | Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation. |
Q27860739 | Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources |
Q34772247 | Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development |
Q31087210 | Systematic interpretation of microarray data using experiment annotations |
Q84543239 | Systemic response to Campylobacter jejuni infection by profiling gene transcription in the spleens of two genetic lines of chickens |
Q33904892 | TAFFEL: Independent Enrichment Analysis of gene sets |
Q42367962 | TET2- and TDG-mediated changes are required for the acquisition of distinct histone modifications in divergent terminal differentiation of myeloid cells. |
Q90557927 | Target 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 |
Q36083151 | Temperature desynchronizes sugar and organic acid metabolism in ripening grapevine fruits and remodels their transcriptome |
Q29615564 | Ten years of pathway analysis: current approaches and outstanding challenges |
Q33365805 | Testing gene set enrichment for subset of genes: Sub-GSE. |
Q28249847 | Text mining for metabolic pathways, signaling cascades, and protein networks |
Q38510213 | Text-based over-representation analysis of microarray gene lists with annotation bias |
Q21184158 | Text-mining and information-retrieval services for molecular biology |
Q38510620 | Text-mining approach to evaluate terms for ontology development |
Q30362316 | The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. |
Q33529113 | The Arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes. |
Q24643720 | The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists |
Q35926110 | The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations |
Q33325831 | The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site |
Q58799510 | The blind men and the elephant: on meeting the problem of multiple truths in data from clustering and pattern mining perspectives |
Q33913372 | The common ground of genomics and systems biology |
Q47407077 | The consequence of natural selection on genetic variation in the mouse |
Q36435183 | The corepressor NCoR1 antagonizes PGC-1α and estrogen-related receptor α in the regulation of skeletal muscle function and oxidative metabolism |
Q33687003 | The distribution of GYR- and YLP-like motifs in Drosophila suggests a general role in cuticle assembly and other protein-protein interactions |
Q39688765 | The effects of two different ganoderma species (Lingzhi) on gene expression in human monocytic THP-1 cells |
Q33695101 | The evolutionary young miR-1290 favors mitotic exit and differentiation of human neural progenitors through altering the cell cycle proteins. |
Q57167930 | The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus |
Q33939198 | The implications of relationships between human diseases and metabolic subpathways |
Q34306294 | The limitations of simple gene set enrichment analysis assuming gene independence |
Q57286200 | The modular network structure of the mutational landscape of Acute Myeloid Leukemia |
Q97517328 | The morbid cutaneous anatomy of the human genome revealed by a bioinformatic approach |
Q36561944 | The peroxisome proliferator-activated receptor γ coactivator 1α/β (PGC-1) coactivators repress the transcriptional activity of NF-κB in skeletal muscle cells |
Q34987266 | The role of the interactome in the maintenance of deleterious variability in human populations |
Q24798755 | The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome |
Q33909410 | Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization |
Q33957849 | ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems |
Q34181781 | Toward a complete in silico, multi-layered embryonic stem cell regulatory network |
Q24811476 | Towards precise classification of cancers based on robust gene functional expression profiles |
Q51248525 | Toxicogenomics in Environmental Science. |
Q55351697 | Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease. |
Q33240474 | Transcription profiles of non-immortalized breast cancer cell lines |
Q34056556 | Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program |
Q34195101 | Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development |
Q90752922 | Transcriptome Characterization of Reverse Development in Turritopsis dohrnii (Hydrozoa, Cnidaria) |
Q36740212 | Transcriptome Response Mediated by Cold Stress in Lotus japonicus |
Q35126175 | Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions |
Q35560029 | Transcriptome and metabolome reprogramming in Vitis vinifera cv. Trincadeira berries upon infection with Botrytis cinerea |
Q93067758 | Transcriptome assembly and annotation of johnsongrass (Sorghum halepense) rhizomes identify candidate rhizome-specific genes |
Q44809252 | Transcriptome-wide identification of RNA binding sites by CLIP-seq |
Q36054045 | Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection |
Q42618762 | Transcriptomic analysis identifies growth rate modulation as a component of the adaptation of mycobacteria to survival inside the macrophage. |
Q33456236 | Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set. |
Q31043070 | Transforming omics data into context: bioinformatics on genomics and proteomics raw data |
Q34422921 | Understanding disease mechanisms with models of signaling pathway activities. |
Q35940326 | Unravelling molecular responses to moderate dehydration in harvested fruit of sweet orange (Citrus sinensis L. Osbeck) using a fruit-specific ABA-deficient mutant |
Q33483794 | Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria |
Q33543998 | Use of microarray technology to assess the time course of liver stress response after confinement exposure in gilthead sea bream (Sparus aurata L.). |
Q50315637 | Using predictive specificity to determine when gene set analysis is biologically meaningful |
Q37455170 | Utility of mass spectrometry for proteome analysis: part II. Ion-activation methods, statistics, bioinformatics and annotation |
Q33402870 | Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. |
Q34550067 | Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis |
Q45905497 | VirtualPlant: a software platform to support systems biology research. |
Q24801533 | Visualization and analysis of microarray and gene ontology data with treemaps |
Q33984285 | Visualizing information across multidimensional post-genomic structured and textual databases |
Q33800456 | Vorinostat interferes with the signaling transduction pathway of T-cell receptor and synergizes with phosphoinositide-3 kinase inhibitors in cutaneous T-cell lymphoma. |
Q36954017 | WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013 |
Q36051062 | Web-based network analysis and visualization using CellMaps |
Q33239646 | Whitefly (Bemisia tabaci) genome project: analysis of sequenced clones from egg, instar, and adult (viruliferous and non-viruliferous) cDNA libraries |
Q38333915 | Whole blood genome-wide expression profiling and network analysis suggest MELAS master regulators |
Q31096199 | Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana |
Q64088316 | Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Uncovers Its Hybrid Origin |
Q38373934 | agriGO: a GO analysis toolkit for the agricultural community |
Q38296436 | cDNA microarray analysis of differentially expressed genes in penile tissue after treatment with tadalafil. |
Q38302104 | g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments |
Q24301438 | hCLE/CGI-99, a human protein that interacts with the influenza virus polymerase, is a mRNA transcription modulator |
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