GO, gene ontology
GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data
... the Gene Ontology (GO) [7] annotations for over-represented ...terms. GO is a standard for functional annotation and consists of structured and controlled vocabularies to classify terms into ...
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Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria
... In order to prepare useful and user friendly reports, we developed logic and data structures in PHP and integrated into Model part of the web application. The major data structure was directed acyclic graph (or tree, if ...
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The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments
... The Gene Ontology (GO) [1,2] contains a set of terms for describing the activity and actions of gene products across all kingdoms of ...the GO includes, since its inception, a ...
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Subtyping of microsatellite instability-high colorectal cancer
... GEO: Gene Expression Omnibus; GO: Gene Ontology; GSEA: Gene set enrichment analyses; HNSCC: Head and neck squamous cell carcinoma; HR: Hazard ratio; KEGG: Kyoto Encyclopedia of Genes ...
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Integrated whole genome microarray analysis and immunohistochemical assay identifies COL11A1, GJB2 and CTRL as predictive biomarkers for pancreatic cancer
... GEO: Gene Expression Omnibus; GSEA: Gene Set Enrichment Analysis; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; PPI: protein– protein interaction; ROC: receiver ...
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GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets
... the GO term ...the GO tree whether from within a software package like GeneSpring GX, or from the web platform AmiGO [12] or a downloadable database ...[13]. GO categories are considered query terms ...
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DisSetSim : an online system for calculating similarity between disease sets
... Disease Ontology; GAD: Genetic Association Database; GeneRIF: Gene Reference into Function; GO: Gene Ontology; GOA: GO annotation; IC: information content; MFSN: miRNA functional ...
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Discovery of MicroRNAs and Transcription Factors Co-Regulatory Modules by integrating Multiple Types of Genomic Data
... of gene products, cellular component where gene products are active, biological process pathways and larger processes made up of the activities of multiple gene ...The Gene Ontology ...
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A semantics-oriented computational approach to investigate microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic leukemia
... as Gene Ontology (GO) [11] annotations, RNAcentral sequence annotations [12], pathway analysis by Protein ANalysis THrough Evolutionary Relationships (PANTHER) Classification System [13], the ...
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Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP
... Trait Ontology (PATO) ...Anatomy Ontology (MA) [20], the Gene Ontology (GO) [24], the Foundational Model of Anatomy Ontology (FMA) [23] and ...
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<p>Weighted Gene Coexpression Network Analysis Identifies Specific Modules and Hub Genes Related to Major Depression</p>
... NCBI Gene Expression Omnibus (GEO) database, including 128 patients with MDD and 64 healthy ...Weighted gene coexpression network analysis (WGCNA) was performed to fi nd modules of differentially expressed ...
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The Drosophila phenotype ontology
... The definition pattern we propose in this system is mod- erately complicated compared to the other formalisms we use. Adding new terms using these patterns manu- ally is more laborious and potentially error-prone than ...
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Loss of non-coding RNA expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines
... 1,317 Gene Ontology (GO) terms in Biological Process for GO process testing and literature-based biomarkers of clinical diseases for GO disease ...partial gene list of subset of ...
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Identification of DNA methylation-driven genes in esophageal squamous cell carcinoma: a study based on The Cancer Genome Atlas
... In our study, we investigated aberrant methylated genes between normal samples and ESCC patients to iden- tify the biomarkers of prognosis related to methylation- driven genes. A model-based tool (methylmix) was used to ...
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The status of causality in biological databases for logical modeling: data resources and data retrieval possibilities
... better informed models, as it informs them on the validity of chaining together several individual causal interactions, whereby the target entity from one causal interaction is used as the source entity for the next one, ...
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Decomposing PPI networks for complex discovery
... localization GO term decomposition method: We utilize cellular component Gene Ontology (GO) terms to decompose PPI networks into several smaller networks such that the proteins in each ...
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Comparative genomics reveals the unique evolutionary status of Plasmodiophora brassicae and the essential role of GPCR signaling pathways
... the GO (Ashburner et ...NCBI, GO, KEGG, and eggNOG databases (Blake and Cohen ...the gene products were presented by Gene Ontology (with a blast E-value of 1e − 6 ...
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Dead simple OWL design patterns
... Biologists classify biological entities in many different ways. A single neuron may be classified by structure (pseudo-bipolar), electrophysiology (spiking), neurotrans- mitter (glutamatergic), sensory modality ...
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The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation
... of GO style—which the Gene Ontology Consortium cites as a factor in its success—is that a com- munity of scientists, ontologists, artificial intelligence experts, and software developers all ...
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Cell specific translational profiling in acute kidney injury
... First, we recovered expected cell type features through bioin- formatics analysis of distinct TRAP populations based on the documented cellular distribution of the CRE-activated EGFP- L10a component. Second, within any ...
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