Applying Steiner minimal tree algorithm in Cytoscape

Question

[anu014]

Hello Biostars!

It's been quite a long time since I posted here. I hope you all are doing great.

This time I need your help in finding sub-network in Protein-Protein Interaction networks (from STRINGdb) using steiner minimal tree algorithm. For this, I want a plugin that I can install directly on Cytoscape. I got 'cyspanningtree' plugin but it doesn't have the required algorithm.

Please do suggest. Thanks in advance! :)

Answer 1

[gary.bader]

Hi - check out the ANAT app - http://apps.cytoscape.org/apps/anatapp and the original paper describing the method: https://www.ncbi.nlm.nih.gov/pubmed/22028466

From the paper: "Given a set of proteins, ANAT seeks a minimum-weight subnetwork H that connects the proteins in this set. The general network construction in ANAT is done in an undirected setting (ignoring edge directions) and uses only edge weights (ignoring node weights). Finding the best network under these settings translates to a Steiner tree problem"

[anu014]

Thanks a lot Gary! It sounds quite promising. I installed ANAT app in Cytoscape. But the 'New Sub-network' option doesn't work somehow for me.. It starts like - 'Retrieving available networks.. Network Problem'. How this can be fixed?

Same for 'New Background Network' option.