The representation of heart development in the gene ontology

• Published in: Developmental biology Vol. 354; no. 1; pp. 9 - 17
• Main Authors: Khodiyar, Varsha K., Hill, David P., Howe, Doug, Berardini, Tanya Z., Tweedie, Susan, Talmud, Philippa J., Breckenridge, Ross, Bhattarcharya, Shoumo, Riley, Paul, Scambler, Peter, Lovering, Ruth C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2011
• Subjects: Animals; Annotation; Cardiovascular; cardiovascular diseases; Cell Differentiation - genetics; community development; Computational Biology - methods; data collection; Databases, Genetic; Development; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Ontology; genes; Genetic Predisposition to Disease; Heart; Heart - embryology; Heart - growth & development; Heart Diseases - genetics; Heart Diseases - pathology; Humans; information retrieval; microarray technology; morphogenesis; Myocardium - cytology; Myocardium - metabolism; proteomics; research and development; signal transduction; Signal Transduction - genetics; stem cells; Vocabulary, Controlled; Heart; Development; Cardiovascular; Annotation; Gene Ontology
• ISSN: 0012-1606; 1095-564X
• DOI: 10.1016/j.ydbio.2011.03.011

An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling. In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development. This work also aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject. The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area. ► The usefulness of high-throughput data depends on the ability to interpret it. ► Gene Ontology (GO) annotations are used to interpret high-throughput data. ► Understanding heart development is important in understanding heart disease. ► We have expanded the available GO terms for heart development from 12 to over 280. ► This dataset could improve interpretation of cardiovascular high-throughput data.