I have a question about the function of Pathway Statistics in PathVisio. After I finished the analysis, a metrics of results is shown.
There is a column called total which shows the total number of genes on the pathway. However, I found the number is not identical to that in the KEGG database.
For instance, the total number of genes in Glycolysis / Gluconeogenesis (ath00010) is 108 while it is 163 in the result metrics.
You are right, the column called total should indeed show the total number
of genes in the pathway.
Could you provide the gpml file for that specific pathway?
On Thu, May 3, 2012 at 9:49 PM, Jia, Qidong <qj...@utk.edu> wrote:
> Hi,
> I have a question about the function of Pathway Statistics in PathVisio.
> After I finished the analysis, a metrics of results is shown.
> There is a column called total which shows the total number of genes on
> the pathway. However, I found the number is not identical to that in the
> KEGG database.
> For instance, the total number of genes in Glycolysis / Gluconeogenesis
> (ath00010) is 108 while it is 163 in the result metrics.
> I don't know where this number comes from.
> Thank you!
> Qidong
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Martina Kutmon, MSc
email: mkut...@gmail.com
skype: mkutmon*
This may be for a number of reasons. First of all, KEGG pathways link to enzyme codes. To calculate the number of genes that correspond to enzyme codes is a non-trivial algorithm that differs somewhat between KEGG and WikiPathways.
Also, depending on the settings of PathVisio, the number in the result metrics may be equal to the number of rows in your expression dataset, not the number of genes in the pathway. If you use for example affymetrix microarray data, it is more than likely that you have several rows in your data set that correspond to a single gene, all of which will be counted in the result metric.
In short, comparing the result metric to the number of genes is not recommended: it's like comparing apples and oranges.
> I have a question about the function of Pathway Statistics in PathVisio. After I finished the analysis, a metrics of results is shown.
> There is a column called total which shows the total number of genes on the pathway. However, I found the number is not identical to that in the KEGG database.
> For instance, the total number of genes in Glycolysis / Gluconeogenesis (ath00010) is 108 while it is 163 in the result metrics.
