Computational Analysis of the Chaperone Interaction Networks

: We provide computational protocols to identify chaperone interacting proteins using a combination of both physical (protein-protein) and genetic (gene-gene or epistatic) interaction data derived from the published large-scale proteomic and genomic studies for the budding yeast Saccharomyces cerevisiae. Using these datasets, we discuss bioinformatic analyses that can be employed to build comprehensive high-fidelity chaperone interaction networks. Given that many proteins typically function as complexes in the cell, we highlight various step-wise approaches for combining both the genetic and physical interaction datasets to decipher intra- and inter-connections for distinct chaperone- and non-chaperone-containing complexes in the network. Together, these informatics procedures will aid in identifying protein complexes with distinctive functional specializations in the cell that yield a very broad and diverse set of interactions. The described procedures can also be leveraged to datasets from other eukaryotes, including humans.