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.

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. :( Marc 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >