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Fig. 1 | BMC Systems Biology

Fig. 1

From: Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines

Fig. 1

Workflow for the methylation and mutation analysis of 30 breast cancer cell lines. A total of 30 breast cancer cell lines representing molecular subtypes of the disease were examined in this study. Analysis starts with quality control and normalization on both MBDcap sequencing data and Affimatrix gene expression data, and methylation and expression level were measured. During integrated analysis, subtype comparison was performed to estimate differentially expressed genes (DEG)s and differentially methylated regions (DMR)s. Experimentally validated transcription factor binding site (TFBS) information is used to estimate TFBS specific methylation level in promoter and CpGI shore overlapped region, and correlation was measured with downstream gene expression. By utilizing mutation information estimated from MBDcap sequencing, subtype specific mutation rate over methylation level was measured. Finally, single base pair resolution bisulfite treatment sequencing was performed to validated the methylation status measured by MBDcap sequencing

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