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