GOseek: A gene ontology search engine using enhanced keywords

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

3 Scopus citations

Abstract

We propose in this paper a biological search engine called GOseek, which overcomes the limitation of current gene similarity tools. Given a set of genes, GOseek returns the most significant genes that are semantically related to the given genes. These returned genes are usually annotated to one of the Lowest Common Ancestors (LCA) of the Gene Ontology (GO) terms annotating the given genes. Most genes have several annotation GO terms. Therefore, there may be more than one LCA for the GO terms annotating the given genes. The LCA annotating the genes that are most semantically related to the given gene is the one that receives the most aggregate semantic contribution from the GO terms annotating the given genes. To identify this LCA, GOseek quantifies the contribution of the GO terms annotating the given genes to the semantics of their LCAs. That is, it encodes the semantic contribution into a numeric format. GOseek uses microarray experiment data to rank result genes based on their significance. We evaluated GOseek experimentally and compared it with a comparable gene prediction tool. Results showed marked improvement over the tool.

Original languageBritish English
Title of host publication2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1502-1505
Number of pages4
ISBN (Print)9781457702167
DOIs
StatePublished - 2013
Event2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013 - Osaka, Japan
Duration: 3 Jul 20137 Jul 2013

Publication series

NameProceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
ISSN (Print)1557-170X

Conference

Conference2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
Country/TerritoryJapan
CityOsaka
Period3/07/137/07/13

Fingerprint

Dive into the research topics of 'GOseek: A gene ontology search engine using enhanced keywords'. Together they form a unique fingerprint.

Cite this