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.

Q:
I have a question about the following excerpt from page 37 of the supp.
materials:

"In this paper, we mainly present a TF-centric analysis. We have also
analyzed other types of genomic contexts, such as gene-centric contexts, to
reveal the effect of context-specific TF co-associations to gene expression,
as well as chromatin state contexts to reveal relationships of TF
co-associations to various enrichments of chromatin marks. We plan to
present these results in a future publication.”

Were those results ever published? If so could you please point me to them.
I’m looking for an updated regulatory networks based on ENCODE data.

A:
try:

http://papers.gersteinlab.org/papers/metatrack
http://papers.gersteinlab.org/papers/loregic