[BioC] KEGGGraph: some complexed proteins are orphans in graphNEL
Paul Shannon
pshannon at systemsbiology.org
Fri May 1 00:23:03 CEST 2009
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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