Hi Paul,

  Thank you so much for the feedback.

  By default, the interactions between complexes are defined by simply
assigning all members of each complex participate in all the interactions
which belong to the complex. I will check the mTOR pathway KGML file and
your kind suggestive evidence to see why TSC1 is orphan after parsing. Then
I will get back to you.

  Best wishes,
David


2009/5/1 Paul Shannon <pshannon@systemsbiology.org>

> We have been using the admirable KEGGGraph package to obtain pathways in
> graphNEL form.  It is very useful.
>
> mTor is the signalling pathway we are working with:
> http://www.genome.jp/dbget-bin/get_pathway?org_name=hsa&mapno=04150
>
> We find that proteins which appear only as members of a complex are orphans
> in the graphNEL.
>
> For instance, "hsa:7248" (TSC1) forms a complex with "hsa:7249" (TSC2).
>  TSC2 is well connected, but its complex partner TSC1
> is an orphan.
>
> There are a number of ways to handle this, some quite sophisticated, some
> not.  Once could define a node for the complex, create edges to that node,
> and then specify (with a 'complex membership' edge) that TSC1 and TSC2 both
> belong.
>
> mTor presents a good (though challenging) use case: there are two
> differently-acting complexes which include mTor and GBL.  The third member
> of the complex is different, however, as are the interactions the two
> complexes participate in.   This seems to argue for 'complex' being a node
> type.
>
> One simple improvement, which solves some of the 'orphan complex node'
> problem, could be this workaround:  all members of each complex participate
> in all the interactions which belong to the complex.
>
> Here is some incomplete (but suggestive) evidence of the orphan status of
> TSC1.  A more detailed search reveals that TSC1 is not found in the target
> nodes of any of the edges of g.mTor.
>
> f <- '~/s/data/public/kegg/hsa04150.xml'
> g.mTor <- parseKGML2Graph (f)
> tsc1 <- 'hsa:7248'
> tsc2 <- 'hsa:7249'
> tsc1 %in% nodes (g.mTor)  #  TRUE
> tsc2 %in% nodes (g.mTor)  #  TRUE
> tsc2 %in% names (edges (g.mTor)) # TRUE
> tsc1 %in% names (edges (g.mTor)) # TRUE
> edges (g.mTor)[[tsc1]]   # character(0)
> edges (g.mTor)[[tsc2]]   # "hsa:6009"
>
> Thanks,
>
>  - Paul
>
>
> sessionInfo ()
>
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> en_US/en_US/en_US/C/en_US/en_US
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] RBGL_1.20.0         gaggle_1.12.0       rJava_0.6-2
> org.Hs.eg.db_2.2.6  RUnit_0.4.22        KEGG.db_2.2.5       RSQLite_0.7-1
>  [8] DBI_0.2-4           AnnotationDbi_1.6.0 Biobase_2.4.0
> KEGGgraph_1.0.0     graph_1.22.0        XML_2.3-0
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.13 tools_2.9.0
>
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>



-- 
Cheers,
David

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