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Assessing identity, redundancy and confounds in Gene Ontology annotations over time.

ABSTRACT: The Gene Ontology (GO) is heavily used in systems biology, but the potential for redundancy, confounds with other data sources and problems with stability over time have been little explored.We report that GO annotations are stable over short periods, with 3% of genes not being most semantically similar to themselves between monthly GO editions. However, we find that genes can alter their 'functional identity' over time, with 20% of genes not matching to themselves (by semantic similarity) after 2 years. We further find that annotation bias in GO, in which some genes are more characterized than others, has declined in yeast, but generally increased in humans. Finally, we discovered that many entries in protein interaction databases are owing to the same published reports that are used for GO annotations, with 66% of assessed GO groups exhibiting this confound. We provide a case study to illustrate how this information can be used in analyses of gene sets and networks.Data available at http://chibi.ubc.ca/assessGO.

SUBMITTER: Gillis J

PROVIDER: S-EPMC3570208 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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Assessing identity, redundancy and confounds in Gene Ontology annotations over time.

Gillis Jesse J Pavlidis Paul P

Bioinformatics (Oxford, England) 20130106 4

<h4>Motivation</h4>The Gene Ontology (GO) is heavily used in systems biology, but the potential for redundancy, confounds with other data sources and problems with stability over time have been little explored.<h4>Results</h4>We report that GO annotations are stable over short periods, with 3% of genes not being most semantically similar to themselves between monthly GO editions. However, we find that genes can alter their 'functional identity' over time, with 20% of genes not matching to themse ...[more]

PMID: 23297035

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Project description:MotivationOntologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other analytical activities. The bio-ontologies community, in particular the Open Biomedical Ontologies (OBO) community, have provided many other ontologies and an increasingly large volume of annotations of gene products that can be exploited in query and analysis. As many annotations with different ontologies centre upon gene products, there is a possibility to explore gene products through multiple ontological perspectives at the same time. Questions could be asked that link a gene product's function, process, cellular location, phenotype and disease. Current tools, such as AmiGO, allow exploration of genes based on their GO annotations, but not through multiple ontological perspectives. In addition, the semantics of these ontology's representations should be able to, through automated reasoning, afford richer query opportunities of the gene product annotations than is currently possible.ResultsTo do this multi-perspective, richer querying of gene product annotations, we have created the Logical Gene Ontology, or GOAL ontology, in OWL that combines the Gene Ontology, Human Disease Ontology and the Mammalian Phenotype Ontology, together with classes that represent the annotations with these ontologies for mouse gene products. Each mouse gene product is represented as a class, with the appropriate relationships to the GO aspects, phenotype and disease with which it has been annotated. We then use defined classes to query these protein classes through automated reasoning, and to build a complex hierarchy of gene products. We have presented this through a Web interface that allows arbitrary queries to be constructed and the results displayed.ConclusionThis standard use of OWL affords a rich interaction with Gene Ontology, Human Disease Ontology and Mammalian Phenotype Ontology annotations for the mouse, to give a fine partitioning of the gene products in the GOAL ontology. OWL in combination with automated reasoning can be effectively used to query across ontologies to ask biologically rich questions. We have demonstrated that automated reasoning can be used to deliver practical on-line querying support for the ontology annotations available for the mouse.AvailabilityThe GOAL Web page is to be found at http://owl.cs.manchester.ac.uk/goal.

Project description:BACKGROUND: Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biological experiments and interpret their results. Despite their importance, these sources of information have some known issues. They are incomplete, since biological knowledge is far from being definitive and it rapidly evolves, and some erroneous annotations may be present. Since the curation process of novel annotations is a costly procedure, both in economical and time terms, computational tools that can reliably predict likely annotations, and thus quicken the discovery of new gene annotations, are very useful. METHODS: We used a set of computational algorithms and weighting schemes to infer novel gene annotations from a set of known ones. We used the latent semantic analysis approach, implementing two popular algorithms (Latent Semantic Indexing and Probabilistic Latent Semantic Analysis) and propose a novel method, the Semantic IMproved Latent Semantic Analysis, which adds a clustering step on the set of considered genes. Furthermore, we propose the improvement of these algorithms by weighting the annotations in the input set. RESULTS: We tested our methods and their weighted variants on the Gene Ontology annotation sets of three model organism genes (Bos taurus, Danio rerio and Drosophila melanogaster ). The methods showed their ability in predicting novel gene annotations and the weighting procedures demonstrated to lead to a valuable improvement, although the obtained results vary according to the dimension of the input annotation set and the considered algorithm. CONCLUSIONS: Out of the three considered methods, the Semantic IMproved Latent Semantic Analysis is the one that provides better results. In particular, when coupled with a proper weighting policy, it is able to predict a significant number of novel annotations, demonstrating to actually be a helpful tool in supporting scientists in the curation process of gene functional annotations.

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Assessing identity, redundancy and confounds in Gene Ontology annotations over time.

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Assessing identity, redundancy and confounds in Gene Ontology annotations over time.

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