Barrett食管和食管腺癌的基因表达谱研究

目的:研究Barrett食管(BE)和食管腺癌的基因表达谱,筛查与食管腺癌相关的基因.方法:使用Dchip软件对已经在GEO数据库中公开的BE和食管腺癌Affymetrix芯片表达谱数据进行分析.还原扫描图像进行独立核验,并对基因和组织进行双向聚类,最后用配对t检验筛查出在BE和食管腺癌中表达水平都发生变化的基因,并进一步分析其功能.结果:24张Affymetrix芯片的杂交质量稳定,被污染和发生交叉杂交的探针簇都少于5%.对基因和样本的双向聚类表明,大部分组织分类正确.只有N8和A5位于错误的组织类型中.对其余22张芯片再次分别进行配对t检验,得到24个基因.其中表达水平呈进行性上升的5个,呈进行性下降的19个.新检出的PITX1已在稍前不久的另一项研究中得到证实.结论:用新的分析方法研究已公开的表达谱芯片资料为研究肿瘤的发病机制提供了新的手段.

Changes of gene expression in Barrett esophagus and adenocarcinoma of esophagus

AIM: To investigate the changes of gene expre- ssion in Barrett esophagus and adenocarci-noma of esophagus. METHODS: A dataset of gene expression profil- ings for 24 paired samples of normal esophageal epithelium, Barrett esophagus and adenocarci- noma of esophagus were downloaded from da- tabase GEO and analyzed with Dchip software. The dataset recovered to raw scanned image was firstly verified. Then the gene expression profil- ings were subjected to gene and sample cluster- ings to identify the contaminated samples. Fi- nally the genes selected by pair-wise t-tests were reviewed for function. RESULTS: The quality of GeneChip hybridiza- tions was good, and the percentages of con- taminated and cross-hybridized probe sets were both below 5%. The gene and sample cluster- ings showed that most of the GeneChips were grouped perfectly except N8 and A5 which were located in wrong clusters. Excluding the two tis- sue contaminated GeneChips, the others weresubjected to pair-wise t-test. Twenty-four genes were finally selected, of which 5 were progres- sively up-regulated in Barrett esophagus and adenocarcinoma of esophagus, while 19 down- regulated. The newly discovered PITX1 that was step-wise down-regulated has been confirmed by a recent study. CONCLUSION: It provides a new way for stu- dying the mechanisms of cancer to reanalyze the publicly accessible datasets of gene expression profiling with new methods.