Q:
I am reading your paper, and have problem about the TF-target gene network data downloaded from http://encodenets.gersteinlab.org/. I want to know which refGene and gene symbol did you use when you find the TF target gene with ChIP-seq data? I find that some symbols are not concluded in hg19 refGene I download from ucsc.

A:
the server was down for a while, and I wasn’t sure what names were you talking about. Now, I think the names are from gencode, but I cannot recall the exact release we used. I believe the names wouldn’t change in general. you can see all the releases here, the names should be in one of the metafiles.
http://www.gencodegenes.org/releases/