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

@article{citeulike:1594838, 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.}, address = {Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China. shaoli@mail.tsinghua.edu.cn}, author = {Li, S. and Wu, L. and Zhang, Z. }, citeulike-article-id = {1594838}, doi = {10.1093/bioinformatics/btl363 }, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {microarray, text-mining}, month = {September}, number = {17}, pages = {2143--2150}, posted-at = {2008-02-26 09:38:27}, priority = {2}, title = {Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16820422}, volume = {22}, year = {2006} }

TY - JOUR ID - citeulike:1594838 L3 - citeulike-article-id:1594838 TI - Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. JF - Bioinformatics VL - 22 IS - 17 SP - 2143 EP - 2150 AD - Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China. shaoli@mail.tsinghua.edu.cn SN - 1460-2059 N2 - 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. KW - microarray KW - text-mining AU - Li, S AU - Wu, L AU - Zhang, Z PY - 2006/09/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/16820422 ER -