Computational protocol: Comprehensive Evaluation of TFF3 Promoter Hypomethylation and Molecular Biomarker Potential for Prostate Cancer Diagnosis and Prognosis

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Protocol publication

[…] Illumina 450K DNA methylation array (450K, 497 RP and 50 matched AN samples), RNA sequencing (RNAseq, 495 RP and 52 matched AN samples), and clinical data were downloaded from The Cancer Genome Atlas (TCGA, http://cancergenome.nih.gov/) () []. The 450K data were peak corrected, as previously described [], and the methylation level for each CpG site was given as a β-value (ranging from 0 to 1). RNAseq data from TCGA were mapped to the human genome (hg19) using Tophat [] and the Bowtie aligner [], and HTSeq [] was used to summarize reads per gene. Gene expression quantified by RNAseq is given as counts per million (CPM).Furthermore, normalized microarray RNA expression data and clinical data were downloaded for 126 PC samples and 29 matched AN samples from GEO (GSE21034; Affymetrix Human Exon 1.0 ST array) [] and for 36 PC and 14 normal prostate samples from GEO (GSE46602; Affymetrix U133 2.0 Plus microarray) []. […]

Pipeline specifications

Software tools TopHat, Bowtie, HTSeq
Databases TCGA Data Portal
Application RNA-seq analysis
Organisms Homo sapiens