Extending gene ontology with gene association networks

Jiajie Peng, Tao Wang, Jixuan Wang, Yadong Wang, Jin Chen

Research output: Contribution to journalArticlepeer-review

44 Scopus citations

Abstract

Motivation: Gene ontology (GO) is a widely used resource to describe the attributes for gene products. However, automatic GO maintenance remains to be difficult because of the complex logical reasoning and the need of biological knowledge that are not explicitly represented in the GO. The existing studies either construct whole GO based on network data or only infer the relations between existing GO terms. None is purposed to add new terms automatically to the existing GO. Results: We proposed a new algorithm 'GOExtender' to efficiently identify all the connected gene pairs labeled by the same parent GO terms. GOExtender is used to predict new GO terms with biological network data, and connect them to the existing GO. Evaluation tests on biological process and cellular component categories of different GO releases showed that GOExtender can extend new GO terms automatically based on the biological network. Furthermore, we applied GOExtender to the recent release of GO and discovered new GO terms with strong support from literature.

Original languageEnglish
Pages (from-to)1185-1194
Number of pages10
JournalBioinformatics
Volume32
Issue number8
DOIs
StatePublished - Apr 15 2016

Bibliographical note

Publisher Copyright:
© 2015 The Author. All rights reserved.

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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