ComPAT: A Comprehensive Pathway Analysis Tools

Pathway annotation or enrichment is often used as the efficient tool to uncover the molecular mechanism of interesting gene sets from genome-wide research. Up to now, numerous pathway databases or web servers that integrated fragmented pathway maps have been published, such as KEGG, Reactome, NetPath, Pathway Commons, DAVID and PathwAX. However, all these data sources are not taking into account the pathway quantity or pathway topology information. Thus, to fill the gap, we developed ComPAT, which provides a web framework that enables users to perform pathway/subpathway enrichment analysis for interesting gene sets, browse and search detailed pathway annotation information. The current version of ComPAT contains a total of 2,881 pathways that were obtained from 10 pathway databases and extended gene interactions from 10 other gene interaction databases, including 10,760 genes and 1,136,971 interactive relationships. All pathways in ComPAT were converted into graphs. ComPAT provides comprehensive annotation for pathways, including network visualization and topology information, gene subcellular localization and gene–gene interaction strength. What's more, ComPAT integrated five types of subpathway algorithms to split pathways into 23,024 subpathways for small-scale gene sets enrichment. Users can input the interesting gene sets for pathway/subpathway annotation or enrichment analysis. Here, we performed the subpathway analysis for cardiac remodeling as a biological case. ComPAT also supports subpathway analysis pipeline for user-input networks. The server is freely available at http://bio.licpathway.net:8018/msg/ComPAT/index.do.