Computational protocol: Tissue Specific DNA Methylation in Normal Human Breast Epithelium and in Breast Cancer

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Protocol publication

[…] Methylation data for the different cancer types were downloaded from The Cancer Genome Atlas (TCGA) portal (https://tcga-data.nci.nih.gov/tcga/) . Level 3 data and clinical annotation tables were downloaded for all samples analyzed with the Illumina Human Methylation 450 k Array. Expression data of the different cancers were downloaded from the UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/proj/site/hgHeatmap/). RNA sequencing data measured by Illumina HiSeq were downloaded whenever available. The colorectal cancer dataset did not contain HiSeq data and gene expression data measured by AgilentG4502_A were downloaded for analysis instead. For the comparison of methylation and gene expression differences between normal and tumor samples, metastatic samples were filtered out using provided annotation data. For the analysis of the breast cancer dataset by subtypes, normal and metastatic samples were removed. Tumors with PAM50 classification information in the TCGA clinical table were used for the analysis. In and the R statistical program was used for statistical analysis and plots were generated using the ggplot2 package . P-values between groups were calculated using Welch's corrected t-test unless otherwise mentioned. Multiple test comparisons were corrected using Bonferroni correction. […]

Pipeline specifications

Software tools UCSC Cancer Genomics Browser, Ggplot2
Databases TCGA Data Portal
Applications Miscellaneous, RNA-seq analysis
Organisms Homo sapiens
Diseases Breast Neoplasms, Carcinoma, Neoplasms, Pancreatic Neoplasms
Chemicals Estrogens