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DAVID Fisher Exact Test contingency table
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2.7 years ago
igor 7.7k
@igor18998

I am looking at the DAVID documentation here and specifically the contingency table: https://david.ncifcrf.gov/content.jsp?file=functional_annotation.html

In DAVID annotation system, Fisher Exact is adopted to measure the gene-enrichment in annotation terms.

In human genome background (30,000 gene total), 40 genes are involved in p53 signaling pathway. A given gene list has found that 3 out of 300 belong to p53 signaling pathway. Then we ask the question if 3/300 is more than random chance comparing to the human background of 40/30000.

screenshot

However, the contingency table shown adds up to 30,300. Isn't it supposed to add up to 30,000? Is that a typo or are there multiple ways to perform the Fisher Exact test?

pathway stats david • 2.5k views
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Looks like a typo. Please let them know.

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I will. Thanks for the suggestion.

I was mostly just concerned that maybe I am not fully understanding Fisher's exact test. I found that page while looking for examples that involve gene set enrichment.

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It still shows the same contingency table.

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2.7 years ago
@Poorya Parvizi22564

Hi!

One gene can be part of more than one Pathway. So, the total number of genes would be higher than the number of Genome. I recommend you to look for the intersection between the genes in "Pathway" and "Not In Pathway".

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You only test one pathway at a time and the sum of the cells in the contingency table must sum to the total number of genes (or the relevant subset) or else you're violating assumptions of the test. I don't even know what it would mean for a gene to be both in and not in a given pathway at the same time...it'd be like a Schrödinger gene or something.

My guess is actually that the second column in the original table isn't really meant to be the second column of the contingency table, but rather the row sums. Then everything would add up correctly.

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"Schrödinger gene"... I will have to work that into a presentation somehow

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