[BioC] Visualizing KEGG pathways

[Saroj K Mohapatra]

Hi Tim:
> # color the pathway accordingly
> url = color.pathway.by.objects(pathstr, glist, fg=fgcols, bg=bgcols)
> My question is whether I can get the actual gene name (in this case 'AKR1A1') instead of '1.1.1.2' on the node that is given in the graph - i.e., how can I get the gene names (for 'hsa') on the graph ?
>   

It would be nice to have that capability. I do not see any way of doing 
that, at least not through these functions: color.pathway.by.objects and 
mark.pathway.by.objects. Perhaps some one else might have an idea.
>   
> [1] 155
>
> This lists 155 genes as being associated with the pathway. But if I go to the KEGG graph ("http://www.genome.jp/kegg/pathway/hsa/hsa04630.html") I just see perhaps 20 nodes/genes. Where is my disconnect?
>   
 >From the link that you provided 
("http://www.genome.jp/kegg/pathway/hsa/hsa04630.html") , I click on 
Pathway entry and reach 
(http://www.genome.jp/dbget-bin/www_bget?pathway+hsa04630). On that 
page, under the category "Gene", these are listed, all 155 (copied 
below). You would notice that there are multiple gene ids for the same 
EC id, e.g., 10000 (AKT3), 207(AKT1) and 208(AKT2) all stand for the 
same EC:2.7.11.1 and are represented by the node AKT on the map.

Best,

Saroj


Tim Smith wrote:
> Hi,
>
> I was trying to explore KEGG pathways. I have two questions:
>
> Question 1:
> -------------
>
>  I used some code given by Saroj:
>
> #---------------------------
>    
> library("KEGGSOAP")
>
> # Suppose you are looking at the pathway for glycolysis / gluconeogenesis
> pathstr = "path:hsa00010"
>
> # get all genes
> glist = get.genes.by.pathway(pathstr)
>
> # First fix what color you want for which node
> # Suppose, you want to color first enzyme hsa:10327 (EC 1.1.1.2)
> # white on blue background and rest all nodes in black on white
> # fgcols = color of text and border
> # bgcols = color of the rectangular area
>
> fgcols = rep("black", length(glist))
> fgcols[1] = "black"
> bgcols = rep("#e6e6fa", length(glist))
> bgcols[1] = "blue"
>
> # color the pathway accordingly
> url = color.pathway.by.objects(pathstr, glist, fg=fgcols, bg=bgcols)
> browseURL(url)
>
> #---------------------------
>
> I get the following graph (with one of the nodes shown as blue) at "http://soap.genome.jp/tmp/mark_pathway_www3_api14519/hsa00010.gif"
>
> The original Glycolysis pathway in KEGG is given at "http://www.genome.jp/kegg/pathway/map/map00010.html"
>
> My question is whether I can get the actual gene name (in this case 'AKR1A1') instead of '1.1.1.2' on the node that is given in the graph - i.e., how can I get the gene names (for 'hsa') on the graph ?
>
>
> Question 2:
> ------------
>
> This is not exactly an R question, so please excuse me - I'm just trying to understand things in KEGG. I used the following code to get the genes for Jak-stat pathway:
>
> #------------
> pathstr = "path:hsa04630"
>
> # get all genes
> glist = get.genes.by.pathway(pathstr)
>
> #------------------
>   
>> length(glist)
>>     
> [1] 155
>
> This lists 155 genes as being associated with the pathway. But if I go to the KEGG graph ("http://www.genome.jp/kegg/pathway/hsa/hsa04630.html") I just see perhaps 20 nodes/genes. Where is my disconnect?
>
> Thanks for the replies!
>
>
>       
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