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Bioinformatics Advance Access originally published online on July 4, 2006
Bioinformatics 2006 22(17):2143-2150; doi:10.1093/bioinformatics/btl363
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach

Shao Li *, Lijiang Wu and Zhongqi Zhang

Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University Beijing 100084, China

*To whom correspondence should be addressed.

Motivation: Network reconstruction of biological entities is very important for understanding biological processes and the organizational principles of biological systems. This work focuses on integrating both the literatures and microarray gene-expression data, and a combined literature mining and microarray analysis (LMMA) approach is developed to construct gene networks of a specific biological system.

Results: In the LMMA approach, a global network is first constructed using the literature-based co-occurrence method. It is then refined using microarray data through a multivariate selection procedure. An application of LMMA to the angiogenesis is presented. Our result shows that the LMMA-based network is more reliable than the co-occurrence-based network in dealing with multiple levels of KEGG gene, KEGG Orthology and pathway.

Availability: The LMMA program is available upon request.

Contact: shaoli{at}mail.tsinghua.edu.cn

Supplementary Information: Supplementary data are available at Bioinformatics online.

Received on February 3, 2006; revised on May 16, 2006; accepted on June 29, 2006

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