PEPPER - Protein complex Expansion using Protein-Protein intERactions

Another offering from the ever-fruitful world of bioinformatics today - with a fruit, fittingly enough.

PEPPER - Protein complex Expansion using Protein-Protein intERactions - pulls out all the stops when it comes to contriving a functional word, skipping words and using internal letters.

For the curious, PEPPER is available from the Cytoscape App Store and is:

“designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network.”

Despite its use of “seed lists”, I don’t think there is a direct connection with peppers, so PEPPER is being classified as an ad hoc intranym.

I’m not sure if there’s a bigger version of the logo available but if you look carefully, you can see the little chilli peppers.

Winterhalter C et al. (2014) PEPPER: cytoscape app for protein complex expansion using protein-protein interaction networks. Bioinformatics. Aug 18. pii: btu517. [Epub ahead of print]