[BioC] KEGG Pathway modules

Marc Carlson mcarlson at fhcrc.org
Tue Apr 20 00:41:49 CEST 2010

Hi Alla,

These IDs are not actually "ko" numbers.  They are "K" numbers.  And
those are not the same thing.  "K" numbers means that they correspond to
KEGG ortholog sets instead of to pathway IDs.  At present we don't have
this data (the ortholog set IDs) available in Bioconductor.  But we are
looking into the possibly of supporting it in the near future. 

Confusingly enough, KEGG refers to the set of pathway IDs that we do
support as the "KEGG Orthology".  Unfortunately, they also refer to
their collection of ortholog IDs as an "orthology" and so it is
extremely easy to get these things mixed up.  :(


On 04/15/2010 08:23 AM, Alla Bulashevska wrote:
> Dear Bioconductor users,
> Pathway modules in KEGG are specification of subnetworks
> that correspond to tighter functional units, each
> represented as a list of KO identifiers (K numbers). 
> For example 
> MODULE: M00307 Ribosome, eukaryotes
> is defined as following list of 79 KO identifiers:
> K02981+K02985+K02984+K02987+K02989+K02991+K02993+K02995+K02997+
> K02947+K02949+K02951+K02953+K02955+K02958+K02957+K02960+K02962+
> K02964+K02966+K02969+K02971+K02973+K02974+K02975+K02976+K02978+
> K02977+K02979+K02980+K02983+K02998+K02925+K02930+K02932+K02934+
> K02937+K02936+K02938+K02940+K02866+K02865+K02868+K02870+K02873+
> K02872+K02875+K02877+K02880+K02883+K02882+K02885+K02889+K02891+
> K02894+K02893+K02896+K02898+K02901+K02900+K02903+K02905+K02908+
> K02910+K02912+K02915+K02918+K02917+K02920+K02922+K02921+K02923+
> K02924+K02927+K02928+K02929+K02941+K02942+K02943
> My question is, how can i retrieve for each module the
> corresponding list of KO identifiers or for the KO
> identifier the Module it belongs to?
> Thank you in Advance,
> Alla Bulashevska,
> University of Freiburg.
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