DocumentCode :
4742
Title :
Determining Semantically Related Significant Genes
Author :
Taha, Kamal
Author_Institution :
Dept. of Electr. & Comput. Eng., Khalifa Univ., Abu Dhabi, United Arab Emirates
Volume :
11
Issue :
6
fYear :
2014
fDate :
Nov.-Dec. 1 2014
Firstpage :
1119
Lastpage :
1130
Abstract :
GO relation embodies some aspects of existence dependency. If GO term xis existence-dependent on GO term y, the presence of y implies the presence of x. Therefore, the genes annotated with the function of the GO term y are usually functionally and semantically related to the genes annotated with the function of the GO term x. A large number of gene set enrichment analysis methods have been developed in recent years for analyzing gene sets enrichment. However, most of these methods overlook the structural dependencies between GO terms in GO graph by not considering the concept of existence dependency. We propose in this paper a biological search engine called RSGSearch that identifies enriched sets of genes annotated with different functions using the concept of existence dependency. We observe that GO term xcannot be existence-dependent on GO term y, if x- and y- have the same specificity (biological characteristics). After encoding into a numeric format the contributions of GO terms annotating target genes to the semantics of their lowest common ancestors (LCAs), RSGSearch uses microarray experiment to identify the most significant LCA that annotates the result genes. We evaluated RSGSearch experimentally and compared it with five gene set enrichment systems. Results showed marked improvement.
Keywords :
bioinformatics; encoding; genetics; search engines; GO graph; GO relation embodies; RSGSearch; biological characteristics; biological search engine; encoding; gene annotation; gene set enrichment analysis; lowest common ancestors; microarray experiment; numeric format; semantically related significant genes; structural dependencies; Bioinformatics; Biological information theory; Biological system modeling; Muscles; Semantics; Statistics; Semantically related genes; gene ontology; gene set enrichment analysis; related genes; semantic similarity;
fLanguage :
English
Journal_Title :
Computational Biology and Bioinformatics, IEEE/ACM Transactions on
Publisher :
ieee
ISSN :
1545-5963
Type :
jour
DOI :
10.1109/TCBB.2014.2344668
Filename :
6868276
Link To Document :
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