This is a supplementary dataset with raw data, scripts, complete analysis files, and supplementary tables/figures for the manuscript entitled "Integrated analysis of “-omic” landscapes in breast cancer subtypes". It is uploaded as a single file archive with the following structure: The Data folder contains TCGA-BRCA omic (RNA-Seq, methylation, CNV, and SNV) processed data and multi-SOM pipeline scripts. The BRCA-TCGA-mlSOM folder contains data and scripts for multi-SOM downstream analysis including functional annotation of gene modules (spots), comparison of their levels in cancer subtypes with true normal tissue, regression analysis for assessment of the association between omic layers, survival, and clinical parameter analysis. The Supplementary data folder contains supplementary tables and figures cited in the text.