Q:
I am very interested in your work on network rewiring. I have been working on experimental validation of network rewiring approaches investigating how this can be used to reprogram regulatory networks to improve heterologous protein production in Yeast. I am now in the process of analysing transcriptional rewiring phenotypes I have identified in a combinatorial library based screen. I have noticed some very interesting enrichment criteria in the groups of rewired promoters and open reading frames with regards to network structure.

I was hoping to look at how these rewired components are natively arranged with regards to their network hierarchy. I would like to use the hierarchical network model you proposed in your paper (http://www.ncbi.nlm.nih.gov/pubmed/21045205?dopt=Abstract) but I have been having trouble reconstructing it from the pdf supplemental data. I am really keen on using your model to study my experimental data further if you have any suggestions on how I could best go about this I would be most greatful.

A:
you might find the following links useful :

http://www.gersteinlab.org/proj/nethierarchy
http://papers.gersteinlab.org/papers/nethierarchy/
website with an earlier version of the yeast hierarchy.

http://papers.gersteinlab.org/papers/mirnet
http://papers.gersteinlab.org/papers/wormawg
information on worm & fly hierarchies

http://papers.gersteinlab.org/papers/encodenets
Human hierarchy

http://papers.gersteinlab.org/papers/callgraph
Bacterial hierarchy

I would also direct you to the wiki page:

http://info.gersteinlab.org/Hierarchy

Under the heading "Phenotypic Effects of Network Rewiring in Transcriptional Regulatory Hierarchies", this page lists all the data in a very user-friendly format that you would need to reproduce the hierarchies with all the datasets very well described/annotated.

This page has the initial regulatory network of E. coli and Yeast and it also provides you with the original breadth-first search hierarchies. In addition, it lists all the changes in the hierarchy upon deletion of each gene. There is an extensive description of what each column in each file means.

Further, in order for you to better understand the algorithm/program we used, I am also attaching a light-weight perl script that generates the hierarchy from a given network (BFS.pl) (it is well annotated with an explanation of each step). I am also attaching another perl script that I used to list the changes the hierarchy upon deletion of each gene (count_changes_modified_hierarchy.pl). Paths will be broken for input files but it should be enough for you to get a flavor of how we quantified changes in the modified hierarchies.