Encode for cancer genomics to predict gene expression

Q:
I am just beginning start my first ever project by using the extended gene definition provided in the dataset of Encode for cancer genomics to predict gene expressions. I would be incredibly grateful if there could be an explanation about the layout of the text files. I have been unsuccessfully trying to understand how the extended gene was used to interpret the mutations and expression changes in the published article.

A:
Thanks for your interest in the research and the extended gene annotation. We are preparing BED-formatted extended gene annotation and they will be available soon on our project website (http://encodec.encodeproject.org/). We will keep you informed.