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Expression differentiation is not helpful in identifying prognostic genes based on TCGA datasets
Molecular Therapy - Nucleic Acids ( IF 8.8 ) Pub Date : 2018-03-06
Ning An, Zhuang Yu, Xue Yang

A routine pipeline seems very common in many cancer studies that expression differentiation might be helpful in identifying prognostic molecules. There also exists a striking unanimity that molecules up-regulated in cancer usually shorten survival, while down-regulated ones have the opposite effect. In this study, based on the transcriptional profiles of 18 malignancies, cancer and corresponding adjacent normal tissues were used to calculate differential score. Cox correlation coefficients of global genes were also calculated to denote survival association. The relationship between expression differentiation and survival association has been extensively studied in 18 malignancy types. Contradictory to our stereotypic research pattern, expression differentiation between cancer and adjacent normal tissues was proven irrelevant to corresponding survival correlation. Surprisingly, the more stringent cutoff we used in differentially expressed gene identification, the less prognostic information we would obtain from the collected gene groups. Moreover, the direction of dysregulated genes in cancer was irrelevant to the direction of corresponding survival correlation. Cancer-normal expression differentiation is irrelevant to genes’ survival correlation in multiple cancers, therefore not helpful in identifying prognostic genes. In future studies, it is more sensible to look into another alternative rather than collect differentially expressed molecules in the initial step.



中文翻译:

表达差异无助于基于TCGA数据集识别预后基因

在许多癌症研究中,一条常规管线似乎非常普遍,即表达差异可能有助于鉴定预后分子。还存在惊人的一致意见,即癌症中上调的分子通常会缩短生存期,而下调的分子则具有相反的作用。在这项研究中,基于18种恶性肿瘤的转录谱,使用癌症和相应的邻近正常组织来计算差异评分。还计算了全局基因的Cox相关系数,以表示存活关联。表达分化和生存关联之间的关系已在18种恶性肿瘤类型中进行了广泛研究。与我们的定型研究模式相反,癌与邻近正常组织之间的表达差异被证明与相应的生存相关性无关。令人惊讶的是,我们在差异表达基因鉴定中使用的严格性越严格,从收集的基因组中获得的预后信息就越少。此外,癌症中基因失调的方向与相应的生存相关性的方向无关。癌症正常表达的分化与多种癌症中基因的生存相关性无关,因此无助于鉴定预后基因。在未来的研究中,比起在最初的步骤中收集差异表达的分子,寻找另一种替代方法更为明智。我们将从收集到的基因组中获得的预后信息越少。而且,癌症中基因失调的方向与相应的生存相关性的方向无关。癌症正常表达的分化与多种癌症中基因的生存相关性无关,因此无助于鉴定预后基因。在未来的研究中,比起在最初的步骤中收集差异表达的分子,寻找另一种选择更为明智。从收集的基因组中获得的预后信息越少。而且,癌症中基因失调的方向与相应的生存相关性的方向无关。癌症正常表达的分化与多种癌症中基因的生存相关性无关,因此无助于鉴定预后基因。在未来的研究中,比起在最初的步骤中收集差异表达的分子,寻找另一种替代方法更为明智。因此无助于鉴定预后基因。在未来的研究中,比起在最初的步骤中收集差异表达的分子,寻找另一种选择更为明智。因此无助于鉴定预后基因。在未来的研究中,比起在最初的步骤中收集差异表达的分子,寻找另一种替代方法更为明智。

更新日期:2018-03-07
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