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

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 applicationof LMMAto the angiogenesis ispresented. Ourresultshows that the LMMA-based network is more reliable than the co-occurrencebased network in dealing with multiple levels of KEGG gene, KEGG Orthology and pathway. Availability: The ILMMA program is available upon request. Contact: shaoli @ mail.tsinghua.edu.cn Supplementary Information: Supplementary data are available all Bioinformatics online.