Thank you for your comment. Accordingly, we counted the number of genes in the network (including those in the our query gene list as well as those added through indirect interactions), as you did in your last IPA usage. We found that the network score was not the number of genes in the network (it was close, though).
According to page 6 of the white paper, "IPA Network Generation Algorithm"
Step 6. The final step is the calculation of p-scores used to rank networks on the IPA "Results" page. The p-scores are derived from p-values. Say there are n gene sin the network and f of them are Focus Genes. The p-value is the probability of finding f or more Focus Genes in a set of n genes randomly selected from the Global Molecular Network. It is calculated using Fisher's exact test as described in section 3, step 6. Since interesting p-values are typically quite low (e.g.: 10-8) it is visually easier to concentrate on the exponent. Therefore, the p-score is defined as:
p-score = -log10(p-value)
I am really not sure whether "p-score" is the same as the network score. When I checked "Results" page, there is no information about "p-value."
I would appreciate your help.
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itsunoda •
Push some randomly sampled gene lists into the calculation and decide for yourself. If the same genes keep coming up in the returned networks, you might want to question its validity
Thank you for your comment. We have an impression that network scores higher than 35 seem to be meaningful. Please let me know your opinion on the network score.
My opinion is that it's too easy to convince yourself what a meaningful score is, in an ultimately unpublishable way. Please do some sanity checks of the form I just described. Merry Christmas