Reproducible Research

APOBEC3B expression in breast cancer reflects cellular proliferation while a deletion polymorphism is associated with immune activation

David W. Cescon*, Benjamin Haibe-Kains* and Tak W. Mak

* Co-first authors


To ensure full reproducibility this work complies with the guidelines proposed by Robert Gentleman [1] in terms of availability of the code and reproducibility of results and figures.

All the analysis code is available from GitHub:

An archive including all the analysis code, data and the GSEA tool is available from here:

Detailed documentation describing how to rerun our analysis pipeline are available here:

The multiple spreadsheets containing the functional annotation clustering (from DAVID) of APOBEC3B co-expressed genes from 17 solid tumor types from TCGA is available here:

Legend: BLCA – Bladder Urothelial Carcinoma; BRCA – Breast Invasive Carcinoma; CESC – Cervical Squamous Cell Carcinoma; COAD – Colon Adenocarcinoma; HNSC – Head and Neck Squamous Cell Carcinoma; KIRC – Kidney Renal Clear Cell Carcinoma; KIRP – Kidney Renal Papillary Cell Carcinoma; LGG – Brain Lower Grade Glioma; LIHC – Liver Hepatocellular Carcinoma; LUAD – Lung adenocarcinoma; LUSC – Lung Squamous Cell Carcinoma; OVCA – Ovarian Serous Cystadenocarcinoma; PRAD – Prostate Adenocarcinoma; SKCM – Skin Cutaneous Melanoma; STAD – Stomach Adenocarcinoma; THCA – Thyroid Carcinoma; UCEC – Uterine Corpus Endometrial Carcinoma.



[1] Robert Gentleman (2005) Reproducible Research: A Bioinformatics Case Study, Statistical Applications in Genetics and Molecular Biology, 4(1):2.