Comparative network analysis via differential graphlet communities

While current protein interaction data provides a rich resource for molecular biology, it mostly lacks condition‐specific details. Abundance of mRNA data for most diseases provides potential to model condition‐specific transcriptional changes. Transcriptional data enables modeling disease mechanisms, and in turn provide potential treatments. While approaches to compare networks constructed from healthy and disease samples have been developed, they do not provide the complete comparison, evaluations are performed on very small networks, or no systematic network analyses are performed on differential network structures. We propose a novel method for efficiently exploiting network structure information in the comparison between any graphs, and validate results in non‐small cell lung cancer. We introduce the notion of differential graphlet community to detect deregulated subgraphs between any graphs such that the network structure information is exploited. The differential graphlet community approach systematically captures network structure differences between any graphs. Instead of using connectivity of each protein or each edge, we used shortest path distributions on differential graphlet communities in order to exploit network structure information on identified deregulated subgraphs. We validated the method by analyzing three non‐small cell lung cancer datasets and validated results on four independent datasets. We observed that the shortest path lengths are significantly longer for normal graphs than for tumor graphs between genes that are in differential graphlet communities, suggesting that tumor cells create "shortcuts" between biological processes that may not be present in normal conditions.