生物信息学在肿瘤研究中的应用.pptVIP

6 SSH Libraries Gene Expresstion Map to Human Genomes(1~22+X) 基因表达图谱 第三十页，共七十二页。 Expression level of genes in SSH libraries Different Colors correspond to different libraries 第三十一页，共七十二页。 Is there a LOH? Expressed in two down-regulated libraries 第三十二页，共七十二页。 LOH map vs. SSH map Lung Cancer Related LOH Lung Cancer Related SSH 第三十三页，共七十二页。 基因芯片数据分析平台 a) 对raw data进行标准化处理，并确定thredshold值(低于该值表示基因不表达，没有杂交信号) b) 结合R/S++，SAS通过生物统计学手段筛选具有显著性差异表达的基因 c) 进一步的芯片分析手段不一而足，可结合具体分析目标进行具体分析。已经做过的分析有：建立从array到全基因组转录图谱，基因表达图谱；聚类分析(hierarchical, SOM and K-means clustering); 结合Gene Ontology, Biocarta, KEGG数据库进行相关pathway分析等 第三十四页，共七十二页。 Normalization 背景知识： 第三十五页，共七十二页。 PathWay Analysis 背景知识： 第三十六页，共七十二页。 分析实例 Genome-wide Gene Expression Map and Analysis of Non-Small Cell Lung Cancer Based on Microarray 第三十七页，共七十二页。 PNAS November 20, 2001 vol. 98 no. 24 第三十八页，共七十二页。 Original Array Data Chip: Human U95A oligonucleotide probe arrays (Affymetrix, SantaClara, CA) 12,600 cDNA clone Sample: Squamous cell lung carcinomas 21 Adenocarcinomas 127 Normal Lung 17 Array data (normalized) 第三十九页，共七十二页。 Analysis Procedures Finding genes from 12,600 cDNA clone Get 7932 genes Flagging the values lower than threshold value About half values keeped Doing T-test with SAS/R for each gene Hierarchical Clustering Divide into two parts: up-regulated and down-regulated Construction of Gene Expression Map and Transcriptome Map 第四十页，共七十二页。 Clustering Result 第四十一页，共七十二页。 肺鳞癌基因表达图谱(3号染色体) 肺鳞癌转录图谱 (3号染色体) 第四十二页，共七十二页。 High-resolution detection of differentially expressed chromosomal regions in NSCLC was obtained by using moving-median method Screening of important NSCLC-related gene Analysis Procedures (Cont.) 第四十三页，共七十二页。 Results 75% (24 of 32) of our results were consistent with the previous studies. And the counterparts in other reports, normally with larger sizes, were narrowed down and many specific genes involved in these region