Q:
I am currently trying to figure out which TFs may be regulating my
modules in the synovium of rheumatoid arthritis patients (generated using
WGCNA of microarray samples). Am I right in understanding I can use your
ENCODE data to do so on this website?

http://encodenets.gersteinlab.org/

Second question is which one of these files should I use to compare my gene
expression module genes with your TF binding gene lists? I noticed the raw
one has huge numbers of genes for each TF, so should I use the other i.e.
filtered?

enets1.Proximal_raw.txt

enets2.Proximal_filtered.txt

Is it a problem the ENCODE TF binding sites are generated from cell lines
and not in the diseased tissue I am interested in? Apologies for my naivety!

A:
quick answers below

…Am I right in understanding I can use your
ENCODE data to do so on this website?

ANSWER: yes

I noticed the raw
one has huge numbers of genes for each TF, so should I use the other i.e.
filtered?

ANSWER: I’d go w/ the filtered one (enets2) first.

Is it a problem the ENCODE TF binding sites are generated from cell lines
and not in the diseased tissue I am interested in?

ANSWER: don’t think so – they are meant to be a ref.