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.
hope this helps,
On 03/05/12 20:49, Jia, Qidong wrote: