It mainly acts on biological processes such as inflammatory response, chemokine metabolic process, and immune response as well ... a) Gene ontology terms of the targets in biological process, (b) Immune system process, and (c) Molecular function. (d) KEGG ... 2.1.4. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Analysis. Following import of the 20 core targets ... M. Kohl, S. Wiese, and B. Warscheid, "Cytoscape: software for visualization and analysis of biological networks," Methods in ...
We apply computational methods to study and develop tools, software, databases and ontologies to manage and analyze high- ...
Gene Ontology (GO) enrichment analysis of the source proteins.. (A) GO enrichment was evaluated by biological process (BP); ... we performed a Gene Ontology (GO) enrichment analysis. As expected, the biological process highlighted the enrichment in ... 2012) clusterProfiler: an R package for comparing biological themes among gene clusters OMICS 16:284-287. ... were attributable to a specific biological process. Indeed, MHC-I peptides are predominantly derived from cytosolic/nuclear ...
Mapping functome leads to gene ontology and the understanding of biological entities. Omics.org http://omics.org/index.php/ ... Biological Computing Division Newsletter, Weizmann Institute of Science, Israel No. 1 May 1996 no longer on the web April 2005 ... Related terms: Functional genomics function, gene function, Gene Ontology; Proteomics protein function ... Marc Vidal Biological Atlas of Functional Maps Cell 104: 333 339, February 9, 2001 Perhaps the "phenome" or phenotype lies ...
Soil Ontology and Informatics (7 p.m. EDT) *Thursday *Biological Data Standards (2 p.m. EDT) ...
Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways. PLoS One. 2017;12:. ... Among those categories, proteolysis and cell wall organization were the largest subcategories in the biological process, ... the k-mers were divided into 3 functional gene ontology categories. ... We determined gene ontology annotations by using the UniProt (https://beta.uniprot.org). ...
GO Gene ontology; BP: Biological process; KEGG: Kyoto Encyclopedia of Genes and Genomes; PCA: Principal component analysis; ... The Gene Ontology and KEGG function enrichment analysis and GSEA were performed using the R package "clusterProfiler". GSVA was ... Biological processes of GO were conducted and to simplify the results, we grouped categories according to functional theme, ... GO analysis was also conducted to assess the biological function of the turquoise module and it involved in B cell regulation ( ...
Histogram of Gene Ontology classification. The results are summarized in three main categories: biological process, cellular ... Since only one biological samples was sequenced, in order to avoid possible high false positive rates we first used trimmed ... Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene ... KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, ...
Gene Ontology (GO) analysis. DAVID20 was used to conducted GO analysis to find out enriched GO terms (cellular components and ... B-C) Biological processes are involved by IgG autoantigens (B) and IgA autoantigens (C). (D) Common cellular components ... When antibody is deposited, it may also impair a number of important biological process in hepatocytes (Figure 6). This ... Gene ontology (GO) enrichment analysis of proteome arrays identified autoantigen enriched unique common cellular components ...
The Biological Entities Content OP locally defines the following ontology elements: Submissions:Biological Entities/biological ... This proposal comes from one of the FAO ontologies developed in the context of the NeOn project. The author of the ontology ... Biological Entities Review ValentinaPresutti. 245456710 April 2008. 20112,011. This revision (revision ID 9212) takes in ... family (owl:Class) A type of biological_entity. It is disjoint with group, order, and species. ...
We can achieve semantic interoperability by relating biological entities to standard terminologies or ontologies. Ontologies ... Ontologies. Depending on the scope of the research area we are working, we develop ontologies and terminologies. We develop ... Knowledge graphs are multimodal, disease-specific and comprise biological entities ranging from the genetic level to the ...
Localization, biological process, and co-expression data are used as powerful indicators for protein-protein interactions. The ... Localization, biological process, and co-expression data are used as powerful indicators for protein-protein interactions. The ... Through this approach, a high number of novel protein-protein interactions with diverse biological roles is discovered. Overall ... Through this approach, a high number of novel protein-protein interactions with diverse biological roles is discovered. Overall ...
The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more ... Get details of an ontology term given its identifer. This workflow uses the EBIs Ontology Lookup Service (OLS) to get the ... Wsdl: http://www.ebi.ac.uk/ontology-lookup/OntologyQuery.wsdl or http://www.ebi.ac.uk/ebisearch/service.ebi?wsdl or http://www. ...
The Species Problem: Biological Species, Ontology, and the Metaphysics of Biology. Lanham : Lexington Books.. ---. 2007. Darwin ... In Aristotles biological writings eidos represents "the dynamic principle of life, an immanent principle of organization and ... "In Defense of Species." Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological ... Although Foucault stages our species being as a "fundamental biological fact," what if we consider the partition of the life ...
... patterns of gene expression and revealed enriched gene ontology biological processes. Within each TCoE set, highly correlated ... 22 major temporal expression patterns of gene expression and were able to show that these patterns associated with biological ...
... gene transcripts were also analysed with the use of gene ontology and pathway analysis approaches to elucidate the biological ... In the biological sciences the suffix -omics is used to refer to the study of large sets of biological molecules.1 The idea ... The Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res 2001;11:1425-33. ... and biological outcomes (the responsome)5 (figure 1). In this context, biological outcomes can be defined as clinical diseases ...
... a database of gene attributes in the context of biological processes in stem cells (Stem Cell Gene Ontology); new software ... This project aims to establish a biological repository of well characterized, induced pluripotent stem cell (iPSC) lines from ... biological discovery and disease treatment in the field. ... methods were undercut by weaknesses in the specific biological ...
This reduces the reliance on existing hierarchical ontologies, the researchers wrote. Lastly, Metascapes enrichment analysis ... lets users compare their lists of genes to thousands of gene sets selected based on their involvement in specific biological ...
A Gene Ontology (biological process) analysis was performed using DAVID functional annotation tools. ... F, Representative Gene Ontology terms of the genes downregulated ,0.5-fold in Tβ4 KO cells. G, Representative microarray data ... F, Representative Gene Ontology terms of the genes downregulated ,0.5-fold in Tβ4 KO cells. G, Representative microarray data ... 4C-E). A Gene Ontology (GO) analysis of downregulated genes in KO cells revealed significant enrichment for terms related to ...
The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show ... we performed over-representation analysis of Gene Ontology (GO) biological processes (BPs) using the R package clusterProfiler ... Gene Ontology (GO) Analysis. To functionally characterize the gene lists corresponding to the intersection of differentially ... Yu, G.; Wang, L.-G.; Han, Y.; He, Q.-Y. ClusterProfiler: An R package for comparing biological themes among gene clusters. ...
He has also participated to the ARDA workshops to build an ontology on video events. In PULSAR team, Fran ois Br mond is ... elderly activity monitoring for homecare applications and wasp monitoring for biological application. ... ontology, Autonomous Systems: real-time systems, system evaluation, parameter tuning, system configuration, system design, 3D ...
... database and ontology development, image analysis, citizen and open science, etc. to analyze all types of biological data.. ... Bio-Ontologies Special Interest Group covers the latest and most innovative research in the application of ontologies and more ... COSIs within this area include: Bio-Ontologies, BioVis, Function, MICROBIOME, MLCSB, NetBio, RegSys, TransMed). Chair: Roded ... COSIs within this area include: Bio-Ontologies, BioVis, CompMS, Evolution and Comparative Genomics, Function, MLCSB, RegSys, ...
Development and application of ontologies for biological applications  Dönitz, Jürgen (2016-02-08) ... Unraveling genetic and epigenetic mechanisms behind various biological processes is possible with Next generation sequencing ( ...
Y. Yamazaki and Jaiswal, P., "Biological ontologies in rice databases. An introduction to the activities in Gramene and ... "The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.", Plant physiology, vol. 143 ... "The Plant Ontology As A Tool For Comparative Plant Anatomy And Genomic Analyses.", Plant & Cell Physiology, 2012. ... "Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.", Comparative and functional genomics, vol ...
Gene ontology functional enrichment analysis revealed twenty eight biological processes and 10 molecular functions associated ... Biological function. FDR. GO:0001505. ACHE, ADORA2A, APP, BCHE, MAOA, MAOB. 6. Regulation of neurotransmitter levels. 3.33E-06 ... Regulation of biological quality. 0.00031. GO:0032222. ACHE, ADORA2A. 2. Regulation of synaptic transmission, cholinergic. ... Gene Ontology (GO) functional enrichment analysis and network pharmacology are the two emerging areas of pharmacology that ...
This regulation included whole process of biological genetic information transmission from chromatin conformation to gene ... BP, biological process; CC, cellular component; DERs, differentially expressed RNA binding protein genes; DEDs, differentially ... The enrichment analysis of Gene Ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were online ... BP, biological process; CC, cellular component; DERs, differentially expressed RNA binding protein genes; DEDs, differentially ...
Ontology:. What does this gene/protein do?. Show (4). PRB2 is implicated in:. - biological_process - cellular_component - ... Biological activities of ER-alpha and ER-beta could be controlled by a number of interacting proteins such as activators/ ... The biological actions of estrogens require their interaction with two estrogen receptors (ER-alpha and ER-beta), which are ... Estrogens exhibit important biological functions and influence several pathological processes of hormone-dependent diseases. ...
Degtyarenko, K., de Matos, P., Ennis, M., et al., ChEBI: A database and ontology for chemical entities of biological interest, ... Batchelor, C., Ontologies for nanotechnology. #237-Technical Sessions, ACS National Meeting March 22-26, 2009, 2009, Salt Lake ... Thomas, D.G., Pappu, R.V., Baker, N.A., et al., Nanoparticle ontology for cancer nanotechnology researches, J. Biomed. Inf., ... Karpova, I., Poryseva, E., Kazakov, G., and Koltsova, E., Development of the ontology in nanocomposite materials, Inf. Resur. ...
The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the host proteins revealed ... the three GO annotation ontologies, i.e., biological process, cellular component, and molecular function, were considered using ... Therefore, the knowledge of interaction mechanisms is crucial to better understand biological processes [20]. Biological ... The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the host proteins revealed ...
Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia ...