Gene ontology
Semantic particularity measure for functional characterization of gene sets using gene ontology.
... Node-based semantic similarity measures rely on how informa- tive the terms are. Typically, they consider that two terms sharing an informative lowest common ancestor are more similar than two terms with a less ...
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Gene Ontology Classification: Building High-level Knowledge using Genetic Algorithms
... Taking into consideration the aforementioned ideas about more suitable classification systems, the rules generated by our proposed GA tend to have a reduced set of antecedents and can be used to predict the class of a ...
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APLICANDO PRINC´IPIOS DE APRENDIZADO DE M ´ AQUINA NA CONSTRUC ¸ ˜ AO DE UM BIOCURADOR AUTOM ´ ATICO PARA O GENE ONTOLOGY (GO)
... Nowadays, the amount of biological data available by universities, hospitals and research centers has increased exponentially due the use of bioinformatics, with the development of methods and advanced computational ...
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Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method.
... Results and Conclusions: Here, we used the IC-based nodes to improve RSS and proposed a new method, Hybrid Relative Specificity Similarity (HRSS). HRSS outperformed other methods in distinguishing true protein-protein ...
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Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.
... A total of 4,006 yeast protein domains shorter than 150 amino acids (a practical length limit for the Rosetta method) and not linked to known structures by PSI-BLAST or fold recognition [r] ...
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Rev. bras. farmacogn. vol.26 número3
... for Gene Ontology (GO) enrichment and protein class using the bioinformatics tools PAN- THER (Mi et ...neighborhood, gene fusion, co-occurrence, co-expression, experiments, database and textmining ...
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Expression analysis of miRNA and target mRNAs in esophageal cancer
... ESCC-related gene expres- sion microarray data for differentially expressed genes; 3) predicting the target genes of differentially expressed miRNAs and constructing regulatory networks depending on the ...
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De novo assembly and characterization of two transcriptomes reveal multiple light-mediated functions in the scallop eye (Bivalvia: Pectinidae).
... For both datasets, sequences were subjected to a series of annotation programs (Fig. 2). First, we applied a four-part blast strategy which uses two different BLAST tools against different publically available databases: ...
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Mesenchymal Stem Cells Exhibit Regulated Exocytosis in Response to Chemerin and IGF.
... Gene ontology, functional enrichment and pathway analysis of the 64 proteins were per- formed using PANTHER with a significance threshold cut-off of ...3B). Gene ontology analysis showed 17 ...
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Transcriptional responses of olive flounder (Paralichthys olivaceus) to low temperature.
... group. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that signal transduction, lipid metabolism, digestive system, and signaling molecules and interaction were the most highly ...
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Bioinformatics Analysis of the Effects of Tobacco Smoke on Gene Expression.
... on gene expression through bioinformatics analyses. Gene expression profile GSE17913 was downloaded from the Gene Expression Omnibus ...identified. Gene Ontology (GO) and pathway ...
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Systems Biology Approach to Study the High Altitude Adaptation in Tibetans
... In order to assess the relative functional enrichment of the genes corresponding to the proteins in the PPIs, the Gene Ontology (GO) Consortium, Genecodis vision 2.0 (Carmona-Saez et al. 2007; ...
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EUROPEAN CONFERNCE ON MACHINE LEARNING AND PRINCIPLES AND PRACTICES OF KNOWLEDGE DISCOVERY IN DATABASES
... The Gene Ontology (GO) dataset used in our work was generated based on the GO portal (http://www.geneontology.org/) [6]. To have a dataset suitable to our goals, we built an SQL statement selecting thirty ...
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Imbalanced multi-modal multi-label learning for subcellular localization prediction of human proteins with both single and multiple sites.
... including gene ontology, functional domain and pseudo amino acid composition, Chou and Cai [43] developed a nearest neighbor algorithm for predicting the subcellular locations of proteins with multiple ...
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Oct4 targets regulatory nodes to modulate stem cell function.
... employed gene expression profiling together with a robust statistical analysis to identify genes highly correlated to Oct4 .... Gene Ontology analysis to categorize overrepresented genes has led to ...
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The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease.
... with gene expression measured by ...levels. Gene ontology (GO) term enrichment analysis of the genes with differential H3K4me3 peaks, revealed statistically significantly enriched GO terms only in ...
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Gene Expression Profile in the Long-Living Lotus: Insights into the Heat Stress Response Mechanism.
... digital gene expression signatures for China Antique lotus under conditions of heat shock ...stress. Gene ontology (GO) enrichment of differentially expressed genes revealed protein folding, cell ...
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Functional annotation of hierarchical modularity.
... (e.g., Gene Ontology) and the association of individual genes or proteins with these concepts ...of gene expression data or protein interaction ...
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Integrative microRNA-gene expression network analysis in genetic hypercalciuric stone-forming rat kidney
... Methods and Results. A multi-step approach combining microarray miRNA and mRNA expression profile and bioinformatics analysis was adopted to analyze dysreg- ulated miRNAs and genes in genetic hypercalciuric stone-forming ...
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