Data received – Re: Your model and input data to the “…integrative analysis of transcription factor binding data” paper

Many thanks for the excellent ENCODE papers! This is an unprecedented source for life scientists, and we appreciate that accordingly!

Would you be so kind as to access your model and input data your random forest model that predicts gene expression based on transcription factor binding?

Could you please also name the source of TSS CAGE? At UCSC, our only suspects were the Riken CAGE*TSS files, or CSHL LongRNA and ShortRNA files.
We would like to run and to adapt your model to the extremely tight co-regulation of ribosome protein genes. We believe that the ENCODE TF’s may account for a major part of their regulation.

Naturally, we would properly cite your works (incl. Cheng & Gerstein, 2011). Should you prefer, we are open to any reasonable forms of collaboration.



The human TSS CAGE data are from Roderic’s Lab.

here is the Human CAGE TSS file:

here is a readme file:

and here are some additional explanations of how the file was made:

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s