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

Shao Li·Lijiang Wu·Zhongqi Zhang
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Abstract

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.

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Abstracting and IndexingDatabase Management SystemsDatabases, ProteinGene Expression ProfilingInformation Storage and RetrievalMEDLINENatural Language ProcessingOligonucleotide Array Sequence AnalysisPeriodicals as TopicProteomeSignal TransductionSystems IntegrationJournal ArticleResearch Support, Non-U.S. Gov't

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Shao Li, Lijiang Wu, Zhongqi Zhang. 2006-07-04. Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach.. https://doi.org/10.1093/bioinformatics%2Fbtl363

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