Gene Ontology (GO) terms
Applicability of semi-supervised learning assumptions for gene ontology terms prediction
... for gene ontology terms prediction ABSTRACT: Gene Ontology (GO) is one of the most important resources in bioinformatics, aiming to provide a unified framework for the biological ...
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MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
... In recent years, numerous computational prediction methods have been developed. Nevertheless, there is still a need for prediction methods that show more robustness and higher accuracy. Results: We extended our previous ...
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UTMGO : a tool for searching a group of semantically related gene ontology terms and application to annotation of anonymous protein sequence
... Abstract— Gene Ontology terms have been actively used to annotate various protein ...the Gene Ontology ...the Gene Ontology terms for annotation of anonymous ...
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Associating Gene Ontology Terms with Pfam Protein Domains
... and Gene ontology (GO) ...GO terms. Therefore, creating a direct mapping between GO terms and Pfam domains will provide a new and more detailed level of protein structure ...GO terms ...
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Searching the gene ontology terms using semantic similarity measure
... III. R EVIEW OF R ELATED W ORK Several GO browsers have been developed to provide text searching over the GO terms and associated information such as definition, synonyms, lineage, cross-references, and ...
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An Integrated Information-Based Similarity Measurement of Gene Ontology Terms
... on gene expression dataset. In the experiment conducted on the gene expression dataset, the performance of our method is evaluated by comparing the semantic similarity values with the gene expression ...
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GO2PUB: Querying PubMed with semantic expansion of gene ontology terms
... In order to verify whether the results from the quali- tative study on lipid metabolism could be generalized to other domains, we submitted twenty randomly-generated queries to GO2PUB and GoPubMed. Each query con- tained ...
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Dependence Relationships between Gene Ontology Terms based on TIGR Gene Product Annotations
... GO ontology than the terms in the antecedent of the rule, since rules containing only terms from one ontology are likely to recover only the term hierarchy of that ontology, which is ...
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GOGO: An Improved Algorithm to Measure the Semantic Similarity Between Gene Ontology Terms
... generic terms without describing particular molecular function, biological process, or cellular ...GO terms, it has the problem that the same GO term may have different IC values when different corpora are ...
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Incorporating semantic similarity measure in genetic algorithm: an approach for searching the gene ontology terms
... GO terms returned by the ...GO terms has been solved by combining semantic similarity measure with genetic ...the ontology search can be easily performed while considering the semantic ...GO ...
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FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences
... Abstract To understand fully cell behaviour, biologists are making progress towards cataloguing the functional elements in the human genome and characterising their roles across a variety of tissues and conditions. Yet, ...
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Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms
... GO terms retrieved from the UniProtKB-GOA database and the terms are weighted using the e-values from BLAST and ...GO terms are processed according to both their semantic similarity relations ...
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ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization
... GO terms in the GO graph reveals that GOmining can consider internal relevant-fea- ture correlation, rather than individual features, by using an efficient global optimization ...GO terms for various ...
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Determining Domain Similarity and Domain-Protein Similarity using Functional Similarity Measurements of Gene Ontology Terms
... scale with information content as fuzzy measure similarity does, meaning that the Dice scores can be artificially high for similar terms with low information content. Average pairwise si[r] ...
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Exercise with Gene Ontology - Cytoscape - BiNGO
... which Gene Ontology terms are overrepresented in gene ...any gene list can be used for this kind of analysis, not only clustered ...
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Primer on the Gene Ontology.
... Part III describes the main strategies used to evaluate their predic- tive performance. Part IV covers practical uses of the GO annota- tions: we discuss how GO terms and GO annotations can be summed and compared, ...
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Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
... of gene product functional attributes, location with phenotype and disease phenomena, such as linking together proteolysis, insulin secretion, plasma membrane, increased glucose concentration and diabetes, is not ...
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Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria
... proteins using a controlled vocabulary in terms of their Molecular Function, Biological Process and Cellular Component. The challenge is to present this information to researchers to compare and discover patterns ...
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The Gene Ontology: enhancements for 2011
... a gene as- sociation file or ...the gene product being annotated, evidence supporting the annotation, the group making the annotation and the GO term associated with the an- ...a gene product and ...
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Exploring autophagy with Gene Ontology.
... those gene products regulate ...existing terms to see if they are speci fic enough to be renamed ‘canonical macroautophagy’ or if they represent a generic form and require additional terms to repre- ...
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