Computational protocol: Silencing of peroxiredoxin II by promoter methylation is necessary for the survival and migration of gastric cancer cells

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Protocol publication

[…] The Cancer Genome Atlas (TCGA) stomach adenocarcinoma (STAD) DNA methylation and mRNA expression data were downloaded at level 3 (that is, as the segmented or interpreted values) from the Broad GDAC Firehose website (released on 28 January 2016). DNA methylation data were obtained for 395 patients using the Illumina Infinium Human Methylation450 or Methylation27 BeadChip technology (San Diego, CA, USA). Transcriptome data were obtained for 415 patients using RNA-Seq experiments on Illumina HiSeq platforms followed by mRNA quantification with the MapSplice-__STRONG_START__RSEM pipeline. Correlation values between PRDX2 gene DNA methylation and gene expression values were calculated as the Pearson correlation coefficient using an R package. For Kaplan–Meier survival analysis, patients were divided into two groups according to their PRDX2 expression value, and the Gehan–Wilcoxon test was performed to obtain statistical significance. [...] Data were expressed as the mean±s.d. and analyzed using Student’s t-test in the SigmaPlot 8.0 software (San Jose, CA, USA). P-value was derived to assess statistical significance. P<0.05 was considered to be statistically significant. […]

Pipeline specifications

Software tools Firebrowse, MapSplice, RSEM, SigmaPlot
Databases TCGA Data Portal
Applications Miscellaneous, RNA-seq analysis
Organisms Homo sapiens, unidentified retrovirus
Diseases Neoplasms, Stomach Neoplasms
Chemicals Hydrogen Peroxide