Discovery of functional module alignment

The alignment of protein interaction networks (PINs) could help reveal similar subnetworks that may play important roles in biology. However, it is challenging to visualize the network alignment, especially for those large-scale PINs. In this work, we present a tool, namely FMA-finder, which can visualize large-scale network alignments between different species. Moreover, instead of focusing on the protein pairs to detect functional homologies, functional module alignment (FMA) is proposed in this study. FMAs are biologically meaningful because they are pairs of subnetworks sharing similar functions. The FMA-finder tool provides both analysis and visualization of FMAs. Experiments on the alignment between Homo sapiens and Saccharomyces cerevisiae protein interaction networks demonstrate that our FMA-finder can visualize and analyze large-scale network alignments.