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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