RGRank: Ranking semantically related genes

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Scopus citations

Abstract

Biologists often need to know the set S' of genes that are semantically related to a given set S of genes. However, most current similarity measures determine the semantic (biological meaning) similarities between the set S rather than identifying the set S̀ Moreover, these similarity measures determine the semantic similarities between the genes based solely on the proximity of their GO term annotations to each other in GO graph while overlooking the structural dependencies between these terms, which may lead to lower recall and precision of results. We propose in this paper a search engine called RGRank, which overcomes the limitations of current similarity measures outlined above as follows: (1) Given a set S of genes, RGRank would return a set Ś of genes, where each gene in S' is semantically related to each gene in S, (2) RGRank ranks gene results by relevance to their semantic similarities to the input genes, and (3) RGRank employs the concept of existence dependency to determine the structural dependencies among the GO terms annotating a given set of gene. We evaluated RGRank experimentally and compared it with three existing methods. Results showed marked improvement.

Original languageBritish English
Title of host publicationProceedings - 15th IEEE International Conference on Computational Science and Engineering, CSE 2012 and 10th IEEE/IFIP International Conference on Embedded and Ubiquitous Computing, EUC 2012
Pages281-288
Number of pages8
DOIs
StatePublished - 2012
Event15th IEEE International Conference on Computational Science and Engineering, CSE 2012 and 10th IEEE/IFIP International Conference on Embedded and Ubiquitous Computing, EUC 2012 - Paphos, Cyprus
Duration: 5 Dec 20127 Dec 2012

Publication series

NameProceedings - 15th IEEE International Conference on Computational Science and Engineering, CSE 2012 and 10th IEEE/IFIP International Conference on Embedded and Ubiquitous Computing, EUC 2012

Conference

Conference15th IEEE International Conference on Computational Science and Engineering, CSE 2012 and 10th IEEE/IFIP International Conference on Embedded and Ubiquitous Computing, EUC 2012
Country/TerritoryCyprus
CityPaphos
Period5/12/127/12/12

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