I tried to analyze PI3K-Akt pathway data from KEGG by Graphite package. But I noticed there are some differences between pathway paradigm on KEGG website http://www.genome.jp/kegg-bin/show_pathway?hsa04151 and downloaded data.
For instance, in paradigm, there is a repression path from FOXO to CCND1. But there is no repression path in data (searched by which(pkegg@edges$type == "Process(repression)")). And there is directed path in data between CCND1 and CDK, which is not presented in paradigm.
Have you guys met this kind of inconsistent problem before?