2016年第43卷第1期目录
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封面故事:肺鳞状细胞癌(LUSC)是主要的肺癌亚型之一,以其常年高居首位的致死率,一直是癌症研究领域的热点和难点.宋凯研究组利用先进的生物信息学方法,首次从全基因组水平综合基因表达(GE)、甲基化水平(ME)和拷贝数变异(CNV)三类数据,分别从特异性、相关性、生物学功能和对肿瘤分类模型的贡献等多个方面,通过迭代降维技术递归筛选真正的特征基因.研究中,以TCGA(The Cancer Genome Atlas project)数据库中的LUSC Ⅰ~Ⅲ期病人样本为例,筛选出67个GE特征基因,对3类样本分类的平均准确率达到86.29%,70个ME特征基因,相应的分类准确率为90.92%,31个CNV特征基因,相应的分类准确率为69.16%.KEGG(Kyoto Encyclopedia of Genes and Genomes)和IPA(Ingenuity Pathway Analysis)对上述3类特征基因的分析,证明了其在调控和代谢水平上的密切关系.
(张 飞,王世祥,王 玲,宋 凯. 肺鳞状细胞癌癌症发展模式识别分类模型及特征基因识别,本期第63~74页)
Cover Story:To identify signature genes for the tumor progression of lung squamous cell carcinoma, which provides a deeper theoretical basis for further explanation of its inherent mechanism, new targeted drugs and treatments development. The pattern recognition method was used to analysis the genome-wide mRNA gene expression (GE) values, methylation values (ME), and copy number variation (CNV) data. To overcome the disadvantages inherent in the genome-wide data such as ultrahigh-dimensional-small-size, high-noise and multi-correlation among genes, and to overcome the predominate influence of the whole genome to the dozens of signature genes, a new iterative multiple variable selection strategy was used to identify signature genes step by step. The importance of genes was comprehensively evaluated by their significant difference with SAM (significant analysis of microarray), statistical analysis using PLS (partial least squares), known biological functions and contributions to the classification model. 67 GE signature genes, 70 ME signature genes and 31 CNV signature genes were identified from the LUSC stageⅠ~Ⅲ patient samples in TCGA (The Cancer Genome Atlas project) database. The corresponding accuracies from 5 fold cross-validation are: 86.29%, 90.92 % and 69.16% respectively. The genetic network analysis and pathway analysis using KEGG (Kyoto Encyclopedia of Genes and Genomes) and IPA (Ingenuity Pathway Analysis) indicated the highly related relationship among these three kinds of genes. They also indicated the immediate relationship between our signature genes and the progression of LUSC which is very important to the understanding of its mechanism and to the development of new targeted therapy.
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综述与专论
研究报告
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