Code repository for the manuscript "Cell type specific functional effects of different BRCA1 and BRCA2 pathogenic mutations in breast and ovarian cancer precursor cells"
Differential Expression Analysis of 8 different conditions
- FT282-BRCA1_OCR vs Control
- FT282-BRCA2_OCR vs Control
- FT282-BRCA1_OCR vs FT282-BRCA2_OCR
- MCF10A-BRCA1_OCR vs Control
- MCF10A-BRCA2_BCR vs Control
- MCF10A-BRCA1_OCR vs MCF10A-BRCA2_BCR
- MCF10A-BRCA1_OCR vs FT282-BRCA1_OCR
- MCF10A-BRCA2_BCR vs FT282-BRCA2_OCR
Countdata.csv - Raw counts used in the statistical programs downstream for differential gene expression where each row is a gene and eash column is a sample.
DESeq2_FT282-BRCA2_OCR vs Controls.r - R code for Differential expression analysis using countdata.
diffexpr-results_Control_vs_BRCA2.csv - Differentially expressed genes results generated from DESeq2 and further used for enrichment analysis.
Enrichment_Analysis.R - Enrihcemnt analysis that generates DotPlots and GOPlots with enrichment GO categories after FDR control.
Mismatch_repair.txt - Mismatch repair pathway genes from KEGG database.
p53_signaling_pathway.txt - p53 signaling pathway genes from KEGG database.
pathway_analysis.R - Specific pathway analysis
- We performed differential expression analysis for each of the eight conditions using the same workflow.