Overview

Goal: In blood cancer cell lines, test whether BRCA1P1 differs by TP53 status (WT vs Mut) at:

RNA expression (CCLE RNA-seq; RPKM; BRCA1P1 is ENSG-based in the GCT)

Copy number (DepMap WGS segment CNV calls; BRCA1P1 is a pseudogene and not in gene-level CN matrices)

We run both RNA and CNV analyses in the same order:

Small panel: 7 blood cancer lines (your focused panel)

All blood cancer lines: full lymphoid + myeloid cohort

## ModelIDs with RP11-242D8.3 RNA:  1019
## All blood cancers (ModelIDs):  351
## ModelIDs with BRCA1P1 RNA:     1019
## # A tibble: 2 × 2
##   TP53_Status     n
##   <chr>       <int>
## 1 Mutant        176
## 2 WT            175

Part I — RNA Expression (CCLE BRCA1P1 RPKM) I-A) Small panel (7-line panel)

## Small panel ModelIDs: 7
## Small panel non-NA RNA: 5
## # A tibble: 2 × 2
##   TP53_Status     n
##   <fct>       <int>
## 1 WT              3
## 2 <NA>            4

BRCA1P1 RNA (RPKM) summary (7-line panel) by TP53 status
Status lower_whisker q1 median q3 upper_whisker n_points
WT 0.081 0.081 0.081 0.081 0.081 1

I-B) All blood cancer lines

## All cohort ModelIDs: 351
## All cohort non-NA RNA: 173
## # A tibble: 2 × 2
##   TP53_Status     n
##   <fct>       <int>
## 1 WT            175
## 2 <NA>          176

BRCA1P1 RNA (RPKM) summary (all blood cancers) by TP53 status
Status lower_whisker q1 median q3 upper_whisker n_points
WT 0 0 0 0 0 68 
## All cohort ModelIDs: 351
## All cohort non-NA RP11 RNA: 173

Part II — Copy number (BRCA1P1 CNV from WGS segments) We extract the CNV segment spanning the BRCA1P1 locus (GRCh38 chr17:43168170–43168249) from OmicsCNSegmentsWGS.csv. Because BRCA1P1 is a pseudogene and not in DepMap gene-level CN matrices, we use WGS segment calls.

## CNV small panel ModelIDs: 7
## CNV small panel with CN segment: 4

BRCA1P1 CNV summary (7-line panel) by TP53 status (log2[1+CN])
Status lower_whisker q1 median q3 upper_whisker n_points
WT 1.005 1.005 1.005 1.005 1.005 1

II-B) All blood cancer lines

## CNV all blood cancers ModelIDs: 351
## CNV all blood cancers with CN segment: 165

BRCA1P1 CNV summary (all blood cancers) by TP53 status (log2[1+CN])
Status lower_whisker q1 median q3 upper_whisker n_points
WT 0.96 1.01 1.023 1.043 1.092 73