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Old 03-21-2014, 10:13 AM   #49
bigmw
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Location: US

Join Date: Aug 2013
Posts: 123
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Shriram,
Here is the original graph from official KEGG website:
http://www.genome.jp/kegg-bin/show_p...e00051+YCL040W
With the GLK1 gene node marked by red box. Hover your mouse over there, do you see 3 budding yeast genes in this nodes: YCL040W (GLK1), YFR053C (HXK1), YGL253W (HXK2)? You may click on this node, and check the details of these genes. Again, the nodes in pathview graphs are labelled with the most representative gene name rather than all mapped gene names for clarity.


Quote:
Originally Posted by shriram View Post
pv.out.list <- sapply(enriched_pathways, function(pid) pathview(gene.data = gene_fc, pathway.id = pid, species = "sce", gene.idtype="KEGG", same.layer = F, kegg.native = T, node.sum="median"))

Data in pathview:
pv.out.list[1]
GLK1 -0.35 0.000 0.620 -1.118 -0.900

# original data supplied for pathview
gene_fc[1,]
GLK 0.14 -1.6 0.62 -1.1 -0.37

I have attached the resultant pathway image.
Original image sce00051.png shows genes specific[in green] to yeast.

I am wondering why pathview data differ for GLK when GLK is the only gene on that node.

Thanks,
Shriram
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