Hi, I was running pathway analysis with a set of differentiated genes on KEGG pathways by SPIA. I tried both SPIA package (version 2.14.0) and graphite package (version 1.8.1). But I found the results from these 2 packages are quite different. For example, the top 3 pathways from the 2 packages are:

1. from SPIA package:

                    Name    ID pSize NDE        pNDE         tA pPERT         pG pGFdr pGFWER    Status
1 mTOR signaling pathway 04150    62   6 0.351094977 -17.835652 0.006 0.01508872     1      1 Inhibited
2             Cell cycle 04110   122  18 0.006213776 -12.637336 0.633 0.02571712     1      1 Inhibited
3 Fanconi anemia pathway 03460    47   8 0.027099800   7.615679 0.207 0.03468601     1      1 Activated

2. from graphite package:
                                    Name pSize NDE       pNDE        tA pPERT         pG     pGFdr pGFWER    Status
1                                Measles    80   6 0.20253998 -26.44386 0.018 0.02411352 0.9830722      1 Inhibited
2            Chemokine signaling pathway   148   8 0.44861958  43.06511 0.010 0.02874194 0.9830722      1 Activated
3 Cytokine-cytokine receptor interaction   199  15 0.06820431  14.58672 0.093 0.03844114 0.9830722      1 Activated

The mTOR pathway that was the top pathway from SPIA package analysis had very different results when analyzed by graphite package:
                      Name pSize NDE     pNDE tA pPERT       pG     pGFdr pGFWER    Status
109 mTOR signaling pathway    53   1 0.932103  0     1 0.997641 0.9999985      1 Inhibited

So is this due to different versions of KEGG databases used in these 2 packages? It appears that mTOR pathway had fewer nodes (53) in graphite package than in SPIA package (62), does that indicate KEGG database is older in graphite package than in SPIA package? The DESCRIPTION file of graphite package indicated the date of version 1.8.1 was 2013-11-03, so appears to be pretty new....

Thanks, any suggestions are appreciated.

John

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