Department of Cell Biology

Interaction Networks

Hierarchical Clustering of the Dub Proteome

A second major goal of our work is to develop proteomic and informatic approaches that allow for the rapid identification of protein interactions within signaling networks and within particular classes of proteins - for example specific classes of ubiquitin pathway genes. We have established a platform for proteomic and informatic analysis of genesets. The centerpiece of this platform is a suite of software called CompPASS which greatly simplifies parallell processing of large proteomic datasets and facilitates the identification of interaction networks. We have applied this methodology to deubiquitinating enzymes, the human autophagy system, cullin RING Ubiquitin Ligases, and many other pathways and genesets.