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

@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. Contact: shaoli@mail.tsinghua.edu.cn Supplementary Information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btl363}, address = {Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China. shaoli@mail.tsinghua.edu.cn}, author = {Li, Shao and Wu, Lijiang and Zhang, Zhongqi}, citeulike-article-id = {1594838}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btl363}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/17/2143}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16820422}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16820422}, citeulike-linkout-4 = {http://dx.doi.org/10.1093/bioinformatics/btl363}, day = {1}, 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://dx.doi.org/10.1093/bioinformatics/btl363}, volume = {22}, year = {2006} }

TY - JOUR ID - citeulike:1594838 L3 - citeulike-article-id:1594838 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. Contact: shaoli@mail.tsinghua.edu.cn Supplementary Information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btl363 IS - 17 JF - Bioinformatics SN - 1460-2059 AD - Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China. shaoli@mail.tsinghua.edu.cn EP - 2150 TI - Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach VL - 22 SP - 2143 KW - microarray KW - text-mining AU - Li, Shao AU - Wu, Lijiang AU - Zhang, Zhongqi PY - 2006/09/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btl363 ER -