Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/89690
Title: Gene ontology enrichment improves performances of functional similarity of genes
Authors: Liu, Wenting
Liu, Jianjun
Rajapakse, Jagath Chandana
Keywords: Gene Ontology
DRNTU::Engineering::Computer science and engineering
Functional Similarity (FS)
Issue Date: 2018
Source: Liu, W., Liu, J., & Rajapakse, J. C. (2018). Gene ontology enrichment improves performances of functional similarity of genes. Scientific Reports, 8(1), 12100-. doi:10.1038/s41598-018-30455-0
Series/Report no.: Scientific Reports
Abstract: There exists a plethora of measures to evaluate functional similarity (FS) between genes, which is a widely used in many bioinformatics applications including detecting molecular pathways, identifying co-expressed genes, predicting protein-protein interactions, and prioritization of disease genes. Measures of FS between genes are mostly derived from Information Contents (IC) of Gene Ontology (GO) terms annotating the genes. However, existing measures evaluating IC of terms based either on the representations of terms in the annotating corpus or on the knowledge embedded in the GO hierarchy do not consider the enrichment of GO terms by the querying pair of genes. The enrichment of a GO term by a pair of gene is dependent on whether the term is annotated by one gene (i.e., partial annotation) or by both genes (i.e. complete annotation) in the pair. In this paper, we propose a method that incorporate enrichment of GO terms by a gene pair in computing their FS and show that GO enrichment improves the performances of 46 existing FS measures in the prediction of sequence homologies, gene expression correlations, protein-protein interactions, and disease associated genes.
URI: https://hdl.handle.net/10356/89690
http://hdl.handle.net/10220/46314
DOI: 10.1038/s41598-018-30455-0
Rights: © 2018 The Author(s) (Nature Publishing Group). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCSE Journal Articles

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