Prediction of multiple drug resistance phenotype in cancer cell lines using gene expression profiles and phylogenetic trees

作     者：LIU XmYi LI ZuoFeng WEN JingRan CAI QingQing XU Ye ZHANG XiaoYan 

作者机构：Department of Bioinformatics School of Life Sciences and Technology Tongji University Shanghai 200092 China Shanghai Center for Bioinformation Technology Shanghai 200235 China Department of Colorectal Surgery Cancer Hospital Fudan University Shanghai 200032 China 

出 版 物：《Chinese Science Bulletin》 (Chin. Sci. Bull.)

年 卷 期：2010年第55卷第33期

页      面：3778-3786页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 0902[农学-园艺学] 090102[农学-作物遗传育种] 090202[农学-蔬菜学] 

基　　金：supported by the National High Technology Research and Development Program of China(2007AA02Z332,2008AA02Z126 and 2009AA02Z308) Shanghai Great Project Program Foundation(07DZ19505) 

主　　题：肿瘤细胞株 基因表达谱 多药耐药 模型预测 表型进化 抗癌药物 系统进化树 基因表达数据 

摘      要：When microarray gene expression data are used to predict multiple drug resistance(MDR)phenotypes for anticancer drugs,the normalization strategy and the quality of the selected signature genes are usually the main causes of inconsistency among different experiments.A stable statistical drug response prediction model is urgently required in *** this study,the microarray gene expression data of multiple cancer cell lines with MDR was *** each probe-set,the expression value was defined as present/absent(1/0)and was classified into a gene set defined with protein domain organization(PDO).After employing the gene content method of phylogenetic analysis,a phylogenetic model(cell tree)for MDR phenotype prediction was built at the PDO gene set *** results indicate that classification of cancer cell lines is predominantly affected by both the histopa-thological features and the MDR phenotype(paclitaxel and vinblastine).When applying this model to predict the MDR phenotype of independent samples,the phylogenetic model performs better than signature gene *** the utility of our procedure is limited due to sample heterogeneity,it still has potential application in MDR research,especially for hematological tumors or established cell lines.