Prediction of essential genes by mining gene ontology semantics

Yu Cheng Liu*, Po I. Chiu, Hsuan Cheng Huang, Vincent S. Tseng

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Essential genes are indispensable for an organism's living. These genes are widely discussed, and many researchers proposed prediction methods that not only find essential genes but also assist pathogens discovery and drug development. However, few studies utilized the relationship between gene functions and essential genes for essential gene prediction. In this paper, we explore the topic of essential gene prediction by adopting the association rule mining technique with Gene Ontology semantic analysis. First, we proposed two features named GOARC (Gene Ontology Association Rule Confidence) and GOCBA (Gene Ontology Classification Based on Association), which are used to enhance the classifier constructed with the features commonly used in previous studies. Secondly, we use an association-based classification algorithm without rule pruning for predicting essential genes. Through experimental evaluations and semantic analysis, our methods can not only enhance the accuracy of essential gene prediction but also facilitate the understanding of the essential genes' semantics in gene functions.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 7th International Symposium, ISBRA 2011, Proceedings
Pages49-60
Number of pages12
DOIs
StatePublished - 16 May 2011
Event7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011 - Changsha, China
Duration: 27 May 201129 May 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6674 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011
CountryChina
CityChangsha
Period27/05/1129/05/11

Keywords

  • Association Rule Mining
  • Data Mining
  • Essential Gene
  • Gene Ontology

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  • Cite this

    Liu, Y. C., Chiu, P. I., Huang, H. C., & Tseng, V. S. (2011). Prediction of essential genes by mining gene ontology semantics. In Bioinformatics Research and Applications - 7th International Symposium, ISBRA 2011, Proceedings (pp. 49-60). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6674 LNBI). https://doi.org/10.1007/978-3-642-21260-4_9