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Old 05-03-2016, 12:13 PM   #1
dawn1313
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Default Pathview for ko

Hi,

I am using Pathview for visualization. But I got the following error

> cnts.dt[,1:3]
K01733 K00615 K08832
[1,] -0.04457192 -0.4192945 -1.1595308
[2,] -0.71249489 -0.9496913 -0.7381559
[3,] -0.01979384 -0.5146385 -0.2218313

> pathview(gene.data = cnts.dt, pathway.id = "01110", kegg.native = T,same.layer = F,species = "ko")
Note: Only KEGG ortholog gene ID is supported, make sure it looks like "K01488"!
Start tag expected, '<' not found
Warning: Parsing ./ko01110.xml file failed, please check the file!


Any thoughts would be appreciated!
Dawn
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Old 05-03-2016, 03:26 PM   #2
dawn1313
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Just to say that after the data transposed I got the same error:

> head(cnts.d)
T1 T2 T3
K01733 -0.04457192 -0.7124949 -0.01979384
K00615 -0.41929452 -0.9496913 -0.51463847
K08832 -1.15953082 -0.7381559 -0.22183132
K02920 -2.02753480 -2.7252426 -0.15968617
K11153 -1.36353517 -1.4521185 -0.92374434
K08266 -1.19325886 -0.9849484 -0.99459590
> pathview(gene.data = cnts.d, pathway.id = "01110", out.suffix = "ko.data",kegg.native = T,same.layer = F,species = "ko")
Note: Only KEGG ortholog gene ID is supported, make sure it looks like "K01488"!
Start tag expected, '<' not found
Warning: Parsing ./ko01110.xml file failed, please check the file!
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Old 05-04-2016, 07:23 AM   #3
wdecoster
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I think you need to specify "K01110" as pathway.id.

That's what it says in the error message: Note: Only KEGG ortholog gene ID is supported, make sure it looks like "K01488"!
And therefore the xml parsing fails afterwards.
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Old 05-08-2016, 03:12 PM   #4
bigmw
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Pathway 01110 is one of the few general pathways, which are very different from the regular ones. For instance, genes/proteins in these pathways are edges instead of nodes (rectangles).
http://www.genome.jp/kegg-bin/show_pathway?ko01110
Therefore, pathview cannot visualize gene data (as in your case) on these few pathways. However, compound data still work.
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Old 05-18-2016, 06:37 PM   #5
dawn1313
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Well all the following pathways, where I have the most hit protiens, not working.

ko01100 Metabolic pathways
ko01110 Biosynthesis of secondary metabolites
ko01130 Biosynthesis of antibiotics
ko01120 Microbial metabolism in diverse environments
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Old 05-20-2016, 07:06 AM   #6
bigmw
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As I said above, these few ones are all general pathways. They are usually the biggest and most inclusive pathway definitions. Therefore, you get most of your protein mapped. But this never means that they are really relevant to your study. You need to do some pathway analysis or enrichment/overrepresentation tests to select the pathway with statistical significance. Very likely, none of these pathways stay relevant.
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Old 05-20-2016, 12:56 PM   #7
dawn1313
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Got it. Thank you!
Just make it clear that the species I study is new. no reference in Kegg, so I used KO terms to have a general idea of regulated genes at pathway level.
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