Question: pathway analysis by SPIA using SPIA package vs graphite package
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5.7 years ago by
array chip360
array chip360 wrote:
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 [[alternative HTML version deleted]]
pathways spia cycle graphite • 883 views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by array chip360
Answer: pathway analysis by SPIA using SPIA package vs graphite package
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gravatar for array chip
5.7 years ago by
array chip360
array chip360 wrote:
actually I found a error in my analysis. the 2 packages now give quite similar results (though not exactly the same). sorry for the confusion John ________________________________ To: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> Sent: Thursday, January 16, 2014 11:34 AM Subject: [BioC] pathway analysis by SPIA using SPIA package vs graphite package 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     [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 5.7 years ago by array chip360
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