Data and Software

You can find source code, documentation, and installation guide for methods developed by our team on the team’s github page: https://github.com/GoekeLab

 

bambu_socialGithub

 

xPore_socialGithub

 

proActiv_githubSocial

 

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

Demircioğlu, D., Cukuroglu, E., Kindermans, M., Nandi, T., Calabrese, C., Fonseca, N. A., Kahles, A., Lehmann, K., Stegle, O., Brazma, A., Brooks, A.N., Rätsch, G., Tan, P., Göke, J.(2019). A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell, 178(6) 1465-1477.

Software:

proActiv: estimate promoter activity using RNA-Seq data

The proActiv R package is available on https://github.com/GoekeLab/proActiv

Gene and Promoter Annotations:

Gene and promoter annotations used in this study can be downloaded here:

The promoter annotation tables can also be generated from any gtf file using proActiv

Data:

The filtered data is available as supplementary material with the publication: https://www.cell.com/cell/fulltext/S0092-8674(19)30906-7

In addition, the results for all promoters before filtering can be downloaded here (https://jglab.org/promoter-data/):

  • Tissue-Specific Promoters
  • Cancer-Associated Promoters
  • Pan-Cancer-Associated Promoters
  • Multi-Cancer type Promoters
  • Molecular Subtype Promoters