[1] Tang Jintao, Wang Ting, Wang Ji,. Discovering hidden information of gene ontologybased on complex networks analysis [J]. Journal of Southeast University (English Edition), 2010, 26 (1): 31-35. [doi:10.3969/j.issn.1003-7985.2010.01007]

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Journal of Southeast University (English Edition)[ISSN:1003-7985/CN:32-1325/N]

Volumn:

26

Issue:

2010 1

Page:

31-35

Research Field:

Computer Science and Engineering

Publishing date:

2010-03-30

Info

Title:

Discovering hidden information of gene ontologybased on complex networks analysis

Author(s):

Tang Jintao¹;  Wang Ting¹;  Wang Ji²

¹School of Computer, National University of Defense Technology, Changsha 410073, China
²National Laboratory for Parallel and Distributed Processing, National University of Defense Technology, Changsha 410073, China

Keywords:

gene ontology;  complex network analysis;  centrality measure

PACS:

TP311

DOI:

10.3969/j.issn.1003-7985.2010.01007

Abstract:

To resolve the ontology understanding problem, the structural features and the potential important terms of a large-scale ontology are investigated from the perspective of complex networks analysis. Through the empirical studies of the gene ontology with various perspectives, this paper shows that the whole gene ontology displays the same topological features as complex networks including “small world” and “scale-free”, while some sub-ontologies have the “scale-free” property but no “small world” effect.The potential important terms in an ontology are discovered by some famous complex network centralization methods.An evaluation method based on information retrieval in MEDLINE is designed to measure the effectiveness of the discovered important terms.According to the relevant literature of the gene ontology terms, the suitability of these centralization methods for ontology important concepts discovering is quantitatively evaluated.The experimental results indicate that the betweenness centrality is the most appropriate method among all the evaluated centralization measures.

References:

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[12] Brian S, Katcher. MEDLINE: a guide to effective searching in PubMed and other interfaces [M]. 2nd ed. San Francisco: Ashbury Press, 2006: 1-136.
[13] Tang Jintao, Wang Ting, Wang Ji, et al. Efficient social network approximate analysis on blogosphere based on network structure characteristics[C]//Proceedings of the Third ACM SNA-KDD Workshop. Paris, France, 2009:55-62.

Memo

Memo:

Biographies: Tang Jintao(1981—), male, graduate; Wang Ting(corresponding author), male, doctor, professor, tingwang@nudt.edu.cn.
Foundation items: The National Basic Research Program of China(973 Program)(No.2005CB321802), Program for New Century Excellent Talents in University(No.NCET-06-0926), the National Natural Science Foundation of China(No.60873097, 90612009).
Citation: Tang Jintao, Wang Ting, Wang Ji. Discovering hidden information of gene ontology based on complex networks analysis[J]. Journal of Southeast University(English Edition), 2010, 26(1): 31-35.

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