Questions about “Architecture of the human regulatory network derived from ENCODE data”

I am reading your paper, and have problem about the TF-target gene network data downloaded from 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.

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.

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