DNA Microarray Data Analysis

我们已经探索了与自发性癌症发展和化学诱导的致癌作用相关的转录模式。在这些研究中，有必要控制混合方向错误发现率，因为我们测试了多重比较，并且在宣布基因上调或下调时可能存在方向错误。 将来自未处理的F344/N大鼠中自发性肿瘤的基因表达模式与来自未处理的年龄匹配的对照动物的样品进行比较。上调的基因与生长因子、癌基因、细胞因子和病原体相关分子模式受体相关。此外，活性氧和氮物质的产生受到影响（黑剪等人，2013年）。凋亡途径下调。为了发现与VDC暴露相关的功能，将对有毒物质偏二氯乙烯产生反应的肿瘤的全局基因表达模式与自发性间皮瘤和F344/N大鼠间皮瘤细胞（Fred-PE）进行比较。从VDC处理的动物产生的数据表明，暴露于这种石棉相关化学物质与致癌基因、生长因子和细胞周期反应的基因调节有关（黑剪等人，2014）。 在另一项研究中，我们评估了心脏和肺组织中与睡眠和睡眠剥夺相关的分子谱。DNA微阵列被用来比较睡眠和睡眠剥夺小鼠组织中的基因表达。总共有3%和6%的测量成绩单被证明是“睡眠特异性”在肺和心脏，分别。与细胞应激和蛋白质折叠相关的过程随着睡眠而减少，而组织特异性代谢过程随着睡眠而增强（Angloman等人，2013年）。

We have explored transcriptional patterns associated with spontaneous cancer development and chemically-induced carcinogenesis. In these studies, it is necessary to control mixed directional false discovery rate due to the fact that we tested for multiple comparisons and there is a potential for directional errors when declaring genes to be up- or downregulated. Gene expression patterns from spontaneous tumors arising in untreated F344/N rats were compared with samples from untreated age-matched control animals. Upregulated genes were associated with growth factors, oncogenes, cytokines, and pathogen-associated molecular patterns receptors. In addition, the production of reactive oxygen and nitrogen species was affected (Blackshear et al., 2013). Apoptosis pathways were downregulated. Global gene expression patterns of tumors arising in response to the toxicant Vinylidene Chloride were compared to spontaneous mesotheliomas and F344/N rat mesothelial cells (Fred-PE) in order to discover the functions associated with VDC exposure. The data produced from VDC-treated animals suggested that exposure to this asbestos-related chemical is associated with the gene regulation of oncogenes, growth factors, and cell cycle response (Blackshear et al., 2014). In a different study, we evaluated the molecular profiles associated with sleep and sleep deprivation in heart and lung tissues. DNA microarrays were used to compare gene expression in tissue from sleeping and sleep deprived mice. A total of 3% and 6% of the measured transcripts were shown to be "sleep specific" in the lung and heart, respectively. Processes associated with cellular stress and protein folding were reduced with sleep, while tissue-specific metabolic processes were enhanced with sleep (Anafi et al., 2013).