Q:

I read your recent paper “Construction and Analysis of an Integrated
Regulatory Network Derived from High-Throughput Sequencing Data” in PLOS
Computational Biology with a great interest. I would like to know if the
data of your integrated regulatory networks is available, or if you mind to
share it. Indeed, I’m part of a group of statisticians in Evry (France)
working on probabilistic models for biological networks. Our aim is to
retrieve the groups of nodes having similar topological behaviours. The
fact that your data has three types of nodes, a hierarchical structure among
TFs and miRNAs and that you made a biological analysis of this structure
makes it very interesting for us to validate or not the methods we
developed. Would it be possible for you to send me the C. elegans network
and the corresponding hierarchical structure? Any use of it would of course
be referenced.

A:

I have upload the worm network data onto http://archive.gersteinlab.org/proj/mirnet
It comprise 3 files:

cel_TF_Target_GID.net : TF->gene interactions
cel_TF_MIR_GID.net: TF->miR interactions
cel_miR_conservedTarget_Kris3way_GID.net: miR->gene interaction

Node type is labeled as “MIR”, “TF” or “X” in the bracket.