Deborah Chasman, Brandi Gancarz, Linhui Hao, Michael Ferris, Paul Ahlquist, Mark Craven
Contact: chasman at cs.wisc.edu or craven at biostat.wisc.edu
This archive contains the code and data used to infer networks for BMV. To run this on your own networks, you will need to produce your own input files.
Due to the limitations of Cytoscape's VizMapper options, some symbols in the Cytoscape files are slightly different than those in the paper. For example, unsigned, directed edges terminate in a diamond rather than a combined arrow/tee. You may need to select "yeast_bmv_background"/"yeast_bmv_inferred" from the VizMapper Visual Style menu.
We used our method to infer a set of high-confidence predictions about which yeast gene products are interfaces with Brome Mosaic Virus. The following images show the neighborhood of each predicted interfaces - that is, all of the pathways in the ensemble that include the interface. Interfaces marked with a frequency of "*" were selected from literature and required to be used as interfaces.