摘要
目的利用生物信息学分析方法寻找结直肠癌(CRC)肝转移生物标志物。方法在公共基因芯片数据库(GEO)下载CRC数据,获得2个数据集共261个样本,其中包含167个非转移样本和94个转移样本,对两批样本混合后随机拆分成训练集195个样本(75%)和验证集66个样本(25%)。对两批数据芯片中提供的原始数据进行Robust Multi-chip Average(RMA)归一化处理,然后利用R-package Combat去除批次效应。筛选在转移组和非转移组t检验P<0.05的基因(426个基因)进行CRC转移相关标志物筛选。结果利用Lasso回归算法对426个基因进行重要性排序,按重要性排序筛选出了CD163L1、FAM210B、LGR5、LRRC16A、PIK3R3、PLEKHA6、PROSER2、RBBP9、SEMA6D、STOM、THBS1、ZNF544前12个基因作为潜在的CRC转移相关标志物。结论通过生物信息学对基因芯片数据的分析,筛选出了CRC肝转移的相关生物标志物,可为后续研究提供参考。
Objective To investigate the application of the bioinformatics method in search for biomarkers for liver metastasis of colorectal carcinoma (CRC).Methods CRC data were downloaded from GEO database,and 261 samples were obtained from 2 datasets,including 167 non-metastatic samples and 94 metastatic samples.These samples were mixed and then randomly divided into training set with 195 samples (75%) and validation set with 66 samples (25%).The raw data provided in two batches of data chips were normalized by Robust Multi-chip Average,and then R-package Combat was used to eliminate the batch effect.A total of 426 differentially expressed genes between the metastasis group and the non-metastasis group (P<0.05) were used to screen out the biomarkers for CRC metastasis.ResultsThe Lasso regression algorithm was used to determine the importance of 426 genes,and CD163L1,FAM210B,LGR5,LRRC16A,PIK3R3,PLEKHA6,PROSER2,RBBP9,SEMA6D,STOM,THBS1,and ZNF544 were identified as the potential markers for CRC metastasis.ConclusionThe bioinformatics method is used to analyze microarray data and screen out the markers for CRC metastasis,which provides a reference for future studies.
作者
金鑫亮
王一休
薛清凯
薛伟杰
宫之奇
牛兆建
朱呈瞻
JIN Xinliang;WANG Yixiu;XUE Qingkai;XUE Weijie;GONG Zhiqi;NIU Zhaojian;ZHU Chengzhan(Department of Gastrointestinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China)
出处
《精准医学杂志》
2018年第6期546-549,554,共5页
Journal of Precision Medicine
基金
国家自然科学基金资助项目(81600490)
山东省科技发展计划项目(2016GGB14019)
中国博士后基金面上项目(2016M602098)
青岛市博士后应用研究项目(2016046)
关键词
计算生物学
数据库
遗传学
结直肠肿瘤
肿瘤转移
肝肿瘤
生物标记
肿瘤
Computational Biology
Databases, genetic
Colorectal neoplasms
Neoplasm metastasis
Liver neoplasms
Biomarkers, tumor
