AIMC Topic: Gene Ontology

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Interspecies gene function prediction using semantic similarity.

BMC systems biology Dec 23, 2016
BACKGROUND: Gene Ontology (GO) is a collaborative project that maintains and develops controlled vocabulary (or terms) to describe the molecular function, biological roles and cellular location of gene products in a hierarchical ontology. GO also pro...
Databases, Genetic Natural Language Processing Zebrafish Animals Mice Computational Biology Molecular Sequence Annotation Gene Ontology Semantics Saccharomyces cerevisiae Species Specificity Humans
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Identifying the missing proteins in human proteome by biological language model.

BMC systems biology Dec 23, 2016
BACKGROUND: With the rapid development of high-throughput sequencing technology, the proteomics research becomes a trendy field in the post genomics era. It is necessary to identify all the native-encoding protein sequences for further function and p...
Humans Probability Protein Transport Gene Ontology Intracellular Space Models, Theoretical Databases, Protein Natural Language Processing Proteomics Proteome
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Grouping miRNAs of similar functions via weighted information content of gene ontology.

BMC bioinformatics Dec 22, 2016
BACKGROUND: Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regu...
MicroRNAs Humans Models, Statistical Algorithms Gene Ontology Gene Expression Profiling Computational Biology Cluster Analysis
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Gogadget: An R Package for Interpretation and Visualization of GO Enrichment Results.

Molecular informatics Dec 21, 2016
Gene expression profiling followed by gene ontology (GO) term enrichment analysis can generate long lists of significant GO terms. To interpret these results and get biological insight in the data, filtering and rearranging these long lists of GO ter...
Sequence Analysis, DNA Cluster Analysis Gene Ontology Software Gene Expression Profiling Computational Biology
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Expansion of the Gene Ontology knowledgebase and resources.

Nucleic acids research Nov 29, 2016
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our conti...
Gene Ontology Databases, Genetic Phylogeny Web Browser Molecular Sequence Annotation Genomics Computational Biology
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Prediction of Protein-Protein Interactions by Evidence Combining Methods.

International journal of molecular sciences Nov 22, 2016
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of c...
Humans Saccharomyces cerevisiae Drosophila melanogaster Computational Biology Arabidopsis Support Vector Machine Computer Simulation Molecular Sequence Annotation Data Mining Gene Ontology Escherichia coli Animals Protein Interaction Mapping High-Throughput Nucleotide Sequencing Mice Proteins Protein Interaction Domains and Motifs Datasets as Topic Models, Molecular
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Analysis of Important Gene Ontology Terms and Biological Pathways Related to Pancreatic Cancer.

BioMed research international Nov 9, 2016
Pancreatic cancer is a serious disease that results in more than thirty thousand deaths around the world per year. To design effective treatments, many investigators have devoted themselves to the study of biological processes and mechanisms underlyi...
Databases, Genetic Humans Pancreatic Neoplasms Signal Transduction Gene Ontology
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SGFSC: speeding the gene functional similarity calculation based on hash tables.

BMC bioinformatics Nov 4, 2016
BACKGROUND: In recent years, many measures of gene functional similarity have been proposed and widely used in all kinds of essential research. These methods are mainly divided into two categories: pairwise approaches and group-wise approaches. Howev...
Computational Biology Programming Languages Semantics Molecular Sequence Annotation Gene Ontology Biomarkers Computer Simulation Genomics Humans Algorithms
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Comprehensive analysis of epigenetically regulated genes in anergic T cells.

Cellular immunology Nov 2, 2016
T cell anergy is one of the important mechanisms for immune tolerance. The results of many studies investigating the mechanism for T cell anergy induction have revealed that the expression of several genes was up-regulated in anergic T cells. It has ...
DNA Methylation Transcriptome Gene Expression Regulation Gene Ontology Mice Humans Th1 Cells Clonal Anergy Epigenesis, Genetic Animals Immune Tolerance
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Combining sequence and Gene Ontology for protein module detection in the Weighted Network.

Journal of theoretical biology Oct 29, 2016
Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating ...
Proteins Gene Ontology Sequence Analysis, Protein
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