iSubpathwayMiner: The package can implement the graph-based reconstruction and analyses of the KEGG pathways

The package can implement the graph-based reconstruction and analysis of the KEGG pathways. (1) Our system provides many strategies of converting pathways to graph models. Ten functions related to conversion from pathways to graphs are developed. Furthermore, the combinations of these functions can get many combined conversion strategies of pathway graphs (> 20). The system can also support topology-based pathway analysis of molecule sets. (2) The iSubpathwayMiner can support the annotation and identification of entire pathways based on molecule (gene and/or metabolite) sets. (3) The iSubpathwayMiner provides the k-clique method for identification of metabolic subpathways based on gene sets. (4) The iSubpathwayMiner provides the Subpathway-GM method for identification of metabolic subpathways based on gene and metabolite sets (new!).

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