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

The package can implement the graph-based reconstruction, analyses, and visualization 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). (2) The iSubpathwayMiner can support the annotation and identification of pathways based on gene sets, compound sets, and even the combined sets of genes and compounds. The entire pathway and subpathway identification methods are available for these sets. (3) The system can also support topology-based pathway analysis of these sets. (4) We develop KEGG layout style of pathway graphs in R to simulate the layout of the pathway picture in KEGG website. In addition, our system has also provided many types of automatic layout styles. Pathway graphs can also be exported to the GML format supported by Cytoscape. (5) The iSubpathwayMiner can provide the most up-to-date pathway analysis results for users. Multiple species (about 139 Eukaryotes, 1141 Bacteria and 93 Archaea) and different gene identifiers (KEGG compound, Entrez Gene IDs, gene official symbol, NCBI-gi IDs, UniProt IDs, PDB IDs, etc.) can also be supported by the system.

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