With the advancement of high-throughput technologies and enrichment of popular public databases, more and more research focuses of bioinformatics research have been on computational integration of network and gene expression profiles for extracting context-dependent active subnetworks. Many methods for subnetwork searching have been developed. Scoring and searching algorithms present a range of computational considerations and implementations. The primary goal of present study is to comprehensively evaluate the performance of different subnetwork detection methods. Eleven popular methods were selected for comprehensive comparison.