Overview

This notebook combines two reviewer-facing analyses across the same cohorts (TNBC/BRCA, PC, OV):

Part I — RNA (CCLE)

Extract BRCA1P1 expression (RPKM) from the CCLE RNA-seq GCT, map CCLE sample IDs to DepMap ModelIDs (ACH-…), and test whether BRCA1P1 expression differs by:

BRCA1 mutation status (WT vs Mut)

BRCA2 mutation status (WT vs Mut)

BRCA1/2 combined (WT vs Mut)

Part II — Copy number (DepMap WGS Segments)

Extract BRCA1P1 copy number from DepMap WGS segmentation calls (BRCA1P1 is a pseudogene; not present in gene-level CN matrices), and test whether BRCA1P1 CN differs by:

BRCA1 mutation status (WT vs Mut)

BRCA2 mutation status (WT vs Mut)

BRCA1/2 combined (WT vs Mut)

Outputs:

Per-cohort plots + summary tables

Per-cohort Excel workbooks

Combined Excel workbook across cohorts (RNA) and across cohorts (CNV)

Part I — RNA expression (CCLE BRCA1P1 RPKM)

## Unique ModelIDs with BRCA1P1 RNA: 1019

RNA TNBC: BRCA12_Status
Status lower_whisker q1 median q3 upper_whisker n_points
Mut 0 0 0 0 0 7
WT 0 0 0 0 0 14

RNA PC: BRCA12_Status
Status lower_whisker q1 median q3 upper_whisker n_points
Mut 0.095 0.128 0.161 0.194 0.227 2
WT 0.000 0.000 0.000 0.000 0.000 6

RNA OV: BRCA12_Status
Status lower_whisker q1 median q3 upper_whisker n_points
Mut 0 0 0 0 0 7
WT 0 0 0 0 0 40

Part II — Copy number (DepMap WGS segments BRCA1P1 CNV)

CNV TNBC: BRCA12_Status
Status lower_whisker q1 median q3 upper_whisker n_points
Mut 0.726 0.847 0.886 1.078 1.424 7
WT 0.684 0.837 0.959 1.088 1.375 15

CNV PC: BRCA12_Status
Status lower_whisker q1 median q3 upper_whisker n_points
Mut 1.012 1.019 1.027 1.075 1.122 3
WT 0.768 0.891 1.013 1.026 1.038 3

CNV OV: BRCA12_Status
Status lower_whisker q1 median q3 upper_whisker n_points
Mut 0.718 0.867 0.934 1.041 1.053 5
WT 0.768 1.006 1.056 1.165 1.404 40