Lee Ding-Dar, Zavadil Jiri, Tomic-Canic Marjana, Blumenberg Miroslav
Department of Dermatology, The NYU Cancer Institute, New York University School of Medicine, New York, NY, USA.
Methods Mol Biol. 2010;585:193-223. doi: 10.1007/978-1-60761-380-0_15.
Because of its accessibility, skin has been among the first organs analyzed using DNA microarrays; psoriasis, melanomas, carcinomas, chronic wound biopsies, and epidermal keratinocytes in culture have been intensely investigated. Skin has everything: stem cells, differentiation, signaling, inflammation, diseases, cancer, etc. Here we provide step-by-step instructions for bioinformatics analysis of transcriptional profiling of skin. Specifically, we describe the use of GCOS and RMA programs for initial normalization and selection of differentially expressed genes, DAVID and LOLA programs for annotation of genes, and statistically relevant identification of over- and under-represented functional and biological categories in identified gene sets, L2L and Venn diagrams for comparing multiple lists of genes, and oPOSSUM for identification of statistically over-represented transcription factor binding sites in the promoter regions of gene sets. The work can be a primer for researchers embarking on skinomics, the comprehensive analysis of transcriptional changes in the skin.
由于皮肤易于获取，它是最早使用DNA微阵列进行分析的器官之一；银屑病、黑色素瘤、癌、慢性伤口活检组织以及培养的表皮角质形成细胞都已得到深入研究。皮肤涵盖了一切：干细胞、分化、信号传导、炎症、疾病、癌症等等。在此，我们提供皮肤转录谱生物信息学分析的详细分步指南。具体而言，我们描述了使用GCOS和RMA程序进行初始标准化和差异表达基因的选择，使用DAVID和LOLA程序进行基因注释，以及对已鉴定基因集中功能和生物学类别过度和不足代表性进行统计学相关鉴定，使用L2L和维恩图比较多个基因列表，使用oPOSSUM鉴定基因集启动子区域中统计学上过度代表性的转录因子结合位点。这项工作可以作为研究人员开展皮肤组学（即对皮肤转录变化进行全面分析）的入门指南。
