Computational protocol: SETD7 is a prognosis predicting factor of breast cancer and regulates redox homeostasis

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Protocol publication

[…] Normalized RSEM RNASeqV2 data and clinical data of breast cancer were downloaded from The Cancer Genome Atlas (TCGA) using TCGA Assembler []. 1086 patients with RNAseq data and clinical survival data were included in this study (). Correlation analysis was employed to examine the relationships between SETD7 and key molecules of KEAP1-NRF2 pathway and ARE target proteins. Log-rank survival analysis was employed to analyze the effect of SETD7 expression and the cross effect between SETD7 and ARE target genes on breast cancer survival. The distribution differences between SETD7 expression and clinicopathological characteristics examined using chi-square test. The effects of clinicopathological characteristics on survival were firstly examined using Log-rank survival analysis, and univariate COX proportional regression was employed to calculate the hazard ratios (HRs) and 95% confidence intervals (95% CIs). Statistically significant variables in univariate analysis were then entered multivariate COX analysis to build a mathematical model using a stepwise conditional method.All experimental data were presented as mean ± standard deviation. One-way analysis of variance (ANOVA) was performed to compare these data between each group and Dunnett's test was employed to avoid family-wise error. A P value less than 0.05 was considered to be statistically significant in this study. Statistical software SAS 9.4 was used to analyze all the data. […]

Pipeline specifications

Software tools RSEM, TCGA-assembler
Databases TCGA Data Portal
Application RNA-seq analysis
Chemicals Glutathione, Glutathione Disulfide