文章流程
- 下載VarScan方法的TCGA的maf突變格式文件
- 計算突變基因，尋找至少在15個樣本都存在突變的基因
- 構(gòu)建突變基因的PPI網(wǎng)絡(luò)
- 突變基因富集分析
- 對突變基因進(jìn)行全部的相關(guān)性分析，識別出，存在相關(guān)性的突變基因。
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
- 相關(guān)性的基因識別出之后，進(jìn)行突變位點的相關(guān)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.對存在相關(guān)性的基因利用在線的Kaplan‐Meier plot 進(jìn)行生存分析
