[BioC] how to find the children identifiers of a specific KEGGidentifier in R??

[Francois Pepin]

Hi Hua,

I've moved the discussion back on the list. This allows other people to
add to the discussion and it is archived so that anyone with a similar
question can find it.

First, GO is hierarchical, so what you get from GOMFCHILDREN or
GOCCCHILDREN are not the member proteins, but more specific GO terms.

You can get it from from the KEGG package:

##hsa03050 is the human proteosome
> get('hsa03050',KEGGPATHID2EXTID)
 [1] "10213" "5682"  "5683"  "5684"  "5685"  "5686"  "5687"  "5688" "5689"
[10] "5690"  "5691"  "5692"  "5693"  "5694"  "5695"  "5700"  "5701"  "5702"
[19] "5704"  "5705"  "5706"  "5707"  "5708"  "5709"  "5710"  "5713"  "5714"
[28] "5717"  "5718"  "5719"  "9861"

those are the EntrezIDs, for the genes. I do not know a direct way to
get the gene names from them in the case of human, although you can go
through one of the microarray annotation package.

If you are already working with one of those packages, you can also get
it the mapping probes directly:

> library(hgu95av2)
> get('03050',hgu95av2PATH2PROBE)
 [1] "33247_at"   "38371_at"   "1446_at"    "41240_at"   "1448_at"
 [6] "1449_at"    "1450_g_at"  "37046_at"   "36122_at"   "33449_at"
[11] "1447_at"    "1310_at"    "1309_at"    "33154_at"   "1311_at"
[16] "37666_at"   "941_at"     "39060_at"   "1313_at"    "688_at"
[21] "35353_at"   "592_at"     "32848_at"   "37766_s_at" "949_s_at"
[26] "1314_at"    "1166_at"    "39155_at"   "39749_at"   "945_at"
[31] "40276_at"   "32584_at"   "1312_at"    "1191_s_at"  "1192_at"
[36] "32211_at"   "34680_s_at"

If you need more help, you might want to tell us a bit more of the
context of what you are trying to do exactly.

Francois

On Wed, 2007-05-16 at 16:19 -0500, Li, Hua wrote:
> Hi, Francois,
>   Yes, if I know one protein in a specific pathway, how to identify
> all the other members?
>   I appreciate your help!!!
> Hua
> 
> ________________________________
> 
> From: Francois Pepin [mailto:fpepin at cs.mcgill.ca]
> Sent: Wed 2007-5-16 16:17
> To: Li, Hua 
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] how to find the children identifiers of a specific KEGGidentifier in R??
> 
> 
> 
> Hi Hua,
> 
> KEGG pathways are not organized hierarchically, they don't have any
> children or ancestors.
> 
> Or are you talking about getting the member genes of a given pathway?
> 
> Francois
> 
> On Wed, 2007-05-16 at 15:27 -0500, Li, Hua wrote:
> > Dear list members:
> >    Once I know a KEGG pathway identifier, how can I check all its
> > direct children identifiers? you know, I could use GOMFCHILDREN or
> > GOCCCHILDREN to check the children terms for a specific GO term, but I
> > don't know how to do it in the same way for KEGG in R?
> >    Many Thanks!!
> > Hua
> >
> > _______________________________________________
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> 
>