WebPropagate is a web-server that implements variants of network propagation on up-to-date PPI networks. Starting from a seed set of proteins that are known to be associated with a process of interest, WebPropagate outputs additional candidate proteins that are significantly associated with the seed set.
WebPropagate offers the use of two key normalization methods for network propagation: RSS (random seed sets), which normalizes the basic propagation scores with 100,000 scores from randomly generated seed sets for each network protein, and RDPN (random degree-preserving networks), which normalizes the basic propagation scores with 1000 scores from randomly generated networks. Both methods produce empirical p-values, correct them for multiple testing and then generate a list of significantly associated proteins based on a user-defined FDR threshold.
We note that due to time considerations, the implementation of RDPN here currently only considers the seed set neighbors as candidates. Further details on both methods, as well as a wide-scale comparison between them and other methods, can be found in [1,2].
WebPropagate also offers two main workflows (both can be done with either RSS or RDPN):
 Biran, H., Almozlino, T., Kupiec, M., and Sharan, R. (2018). WebPropagate: a web-server for network propagation. J. Mol. Biol. 430, 2231–2236. doi: 10.1016/j.jmb.2018.02.025
 Biran, H., Kupiec, M., and Sharan, R. (2019). Comparative Analysis of Normalization Methods for Network Propagation. Front. Genet. 10,4. doi: 10.3389/fgene.2019.00004
Last updated on 2019-02-20 based on BioGRID 3.5.169.