Reconstruction of protein–protein interaction networks using homology-based search: Application to the autophagy pathway of aging in podospora anserina

Abstract

The integration of the available experimental data represents a main problem in systems biology. In particular, in medical sciences, many new data became available, but often data are incomplete and of different quality and quantity. Here, we describe a method for the automatic derivation of protein–protein interaction networks based on homology search, which is applicable to arbitrary pathways and species. We implemented the method as a freely available open-source R package. To demonstrate the application of the method, we consider the autophagy pathway in the filamentous fungus Podospora anserina, which represents an established model organism to unravel the mechanisms of biological aging. Further, we apply network analysis methods to prove the reliability of the network.