Algorithms to identify protein complexes from high-throughput data

W. Rungsarityotin

Ph.D. Thesis, Freie Universität Berlin, Nov 2007.

ecent advances in proteomic technologies such as two-hybrid and biochemical purification allow large-scale investigations of protein interactions. The goal of this thesis is to investigate model-based approaches to predict protein complexes from tandem affinity purification experiments. We compare a simple overlapping model to a partitioning model. In addition, we propose a visualization framework to delineate overlapping complexes from experimental data. We propose two models to predict protein complexes from experimental data. Our first model is in some sense the simplest possible one. It is based on frequent itemset mining, which merely counts the incidence of certain sets of proteins within the experimental results. The affinity of two sets of proteins to form clusters is modeled to be independent, regardless of any overlapping members between these sets. Our second model assumes that formation of protein complexes can be reduced to pairwise interactions between proteins. Interactions between proteins are more likely for pairs of proteins if they come from the same cluster. Based on this model, we use Markov Random Field theory to calculate a maximum-likelihood assignment of proteins to clusters.