CDK11 Study — Repository

Code and analysis scripts accompanying the following preprint:

Julian LA, Crozier L, Lukow D, et al. On-target toxicity limits the efficacy of CDK11 inhibition against cancers with 1p36 deletions. bioRxiv. 2025;2025.08.03.668359. Published 2025 Aug 3. doi:10.1101/2025.08.03.668359

Contents

• Intron retention
  Analysis code is located in the Figure2/Intron-Retention/ directory. Configuration files for reproducing Figure 2 are in Figure2/Intron-Retention/config.

• ChIP-seq analysis
  Analysis code is located in Supplementary Figs/ChIP-seq-FigureS4. Configuration files for reproducing Figure S4 are in Supplementary Figs/ChIP-seq-FigureS4/config.

• Biomarker analysis
  Analysis code is located in the Figure4 directory. Configuration files for reproducing Figure 4 are in Figure4/config.

• Figure generation
  Jupyter notebooks used to generate the manuscript figures.

  • Figure2/Figure2.ipynb
  • Figure4/Figure4.ipynb
  • Supplementary Figs/FigureSupplemental.ipynb

• Data

  • Data used to generate the figures are available in the data subdirectory.
  • Public datasets can be obtained from the DepMap portal and TCGA.

---

Dependencies

The analyses were developed and tested with the following software versions:

Package	Version
Python	3.10
pandas	2.0.3
numpy	1.23.0
scipy	1.10.1
matplotlib	3.7.3
seaborn	0.11.0
PyYAML	5.3.1
deepTools	latest compatible version
yq	latest compatible version

---

PSI-Sigma

Alternative splicing analysis was performed using PSI-Sigma v2.1.

PSI-Sigma was executed from a Singularity container. Please refer to the PSI-Sigma GitHub repository for instructions on obtaining and running the Singularity image.