Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space
Joint Authors
Kim, Ju Han
Kim, Jihun
Kim, Keewon
Source
Computational and Mathematical Methods in Medicine
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-05-03
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Background.
Interpretation of microarray data remains challenging because biological meaning should be extracted from enormous numeric matrices and be presented explicitly.
Moreover, huge public repositories of microarray dataset are ready to be exploited for comparative analysis.
This study aimed to provide a platform where essential implication of a microarray experiment could be visually expressed and various microarray datasets could be intuitively compared.
Results.
On the semantic space, gene sets from Molecular Signature Database (MSigDB) were plotted as landmarks and their relative distances were calculated by Lin’s semantic similarity measure.
By formal concept analysis, a microarray dataset was transformed into a concept lattice with gene clusters as objects and Gene Ontology terms as attributes.
Concepts of a lattice were located on the semantic space reflecting semantic distance from landmarks and edges between concepts were drawn; consequently, a specific geographic pattern could be observed from a microarray dataset.
We termed a distinctive geography shared by microarray datasets of the same category as “semantic signature.” Conclusions.
“Semantic space,” a map of biological entities, could serve as a universal platform for comparative microarray analysis.
When microarray data were displayed on the semantic space as concept lattices, “semantic signature,” characteristic geography for a microarray experiment, could be discovered.
American Psychological Association (APA)
Kim, Jihun& Kim, Keewon& Kim, Ju Han. 2016. Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space. Computational and Mathematical Methods in Medicine،Vol. 2016, no. 2016, pp.1-10.
https://search.emarefa.net/detail/BIM-1100148
Modern Language Association (MLA)
Kim, Jihun…[et al.]. Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space. Computational and Mathematical Methods in Medicine No. 2016 (2016), pp.1-10.
https://search.emarefa.net/detail/BIM-1100148
American Medical Association (AMA)
Kim, Jihun& Kim, Keewon& Kim, Ju Han. Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space. Computational and Mathematical Methods in Medicine. 2016. Vol. 2016, no. 2016, pp.1-10.
https://search.emarefa.net/detail/BIM-1100148
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1100148