elelab / ambra_low Goto Github PK

Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark

Repository associated to the publication:

AMBRA1 regulates cyclin D to guard S-phase entry and genomic integrity. Maiani E, Milletti G, Nazio F, Holdgaard SG, Bartkova J, Rizza S, Cianfanelli V, Lorente M, Simoneschi D, Di Marco M, D'Acunzo P, Di Leo L, Rasmussen R, Montagna C, Raciti M, De Stefanis C, Gabicagogeascoa E, Rona G, Salvador N, Pupo E, Merchut-Maya JM, Daniel CJ, Carinci M, Cesarini V, O'sullivan A, Jeong YT, Bordi M, Russo F, Campello S, Gallo A, Filomeni G, Lanzetti L, Sears RC, Hamerlik P, Bartolazzi A, Hynds RE, Pearce DR, Swanton C, Pagano M, Velasco G, Papaleo E, De Zio D, Maya-Mendoza A, Locatelli F, Bartek J, Cecconi F. Nature. 2021 Apr;592(7856):799-803. doi: 10.1038/s41586-021-03422-5.

for information on the repository: Elena Papaleo, elenap-at-cancer.dk

This repository contains curated RNASEQ data from tumor and normal solid tissue samples obtained from TCGA, and analyzed as legacy data. The repository was made with the intent of openly sharing both the data used at the time of the analyses and the R-scripts employed to carry out the study. The analysis were carried out in August 2017.

1. the R script includes the code to download the samples of the group of interest and perfom Differential Expression Analyses
2. the xls file includes the summary with the statistics of AMBRA1 expression level to define 'AMBRA low' samples
3. the pdf is a visual representation of the expression levels of CHK1 in the cocorresponding groups.

Requirements:

R version 3.3.1 or higher Rstudio version 1.1.383 or higher Bioconductor version 3.6 or higher

Other packages required:

BIOCONDUCTOR:

TCGAbiolinks SummarizedExperiment

a) We suggest to use Rstudio to run the scripts of interest so that you can follow the analyses one line at the time and digest the results.