SNP mutation‐related genes in br

文章流程

1. 下载VarScan方法的TCGA的maf突变格式文件
2. 计算突变基因，寻找至少在15个样本都存在突变的基因
3. 构建突变基因的PPI网络
4. 突变基因富集分析
5. 对突变基因进行全部的相关性分析，识别出，存在相关性的突变基因。

The correlation analysis revealed correlations be- tween the mutation and expression of six genes (NCOR1, GATA3, CDH1, ATM, AKT1, and PTEN). Among them, the expression levels of CDH1, NCOR1, ATM, and PTEN in the mutant samples were decreased, while the expres- sion of GATA3 and AKT1 increased

6. 相关性的基因识别出之后，进行突变位点的相关性分析

In addition, further site analysis revealed that mutations in AKT1 rs121434592, CDH1 rs587783047, and GATA3 rs763236375 were significantly associated with cor- responding gene expression (Figure 6). Limited by the sample size, the gene NCOR1, ATM, and PTEN mutation sites samples were too small, leading to the failure to find the mutation sites that affect gene expression, and further exploration is needed later.

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7.对存在相关性的基因利用在线的Kaplan‐Meier plot 进行生存分析