Q:
I recently read your article “Construction
and Analysis of an Integrated Regulatory Network Derived from
High-Throughput Sequencing Data”. In the last year, I measured mRNA and
miRNA expression in the different types of mouse skeletal muscle fibers to
discover the different regulatory circuits activated in fast and slow
myofibers. I designed a preliminary network using the databases of miRNA –
target mRNA and protein – protein interactions, and I have started to
include my expression data in order to understand the biological meaning. I
was wondering if it is possible to use your more accurate mouse regulatory
network for my data. Is this network free to use? In the article and in the
website of your laboratory I did not find any file or link with the complete
networks that you describe. I am not a computational biologist, but the
paper is very interesting and I think that the network that you design with
your method could be very useful for the scientific community.

A:
Hereby I attach three files for our three mouse networks. 1) how miRNAs targeting genes (This is not our calculation, but downloaded from TargetScan).
2) how TFs targeting genes, 3) how TFs targeting miRNAs based on ChIP-Seq data of 12 TFs.
The files are in plain text format. The first column is the list of regulators and the second column is the list of targets. The bracket next to a gene name gives the class of the gene, TF for transcription factors, MIR for miRNAs, and X for non-TF protein-coding genes.
Thank you for your interest of our paper. I hope this information will be useful for your work.