Last updated on 11:07 PM 9/26/22 by «GreetingLine»
How GO::TermFinder calculates P-values
The GO::TermFinder attempts to determine whether an observed level of annotation for
a group of genes is significant within the context of annotation for all genes within the
genome. Suppose that we have a total population of N genes, in which M have a
particular annotation. If we observe x genes with that annotation, in a sample of n
genes, then we can calculate the probability of that observation, using the
hypergeometric distribution (e.g., see
http://mathworld.wolfram.com/HypergeometricDistribution.html) as:
where generically,
which is the number of permutations by which r entities can be selected from n entities,
is calculated as:
To actually generate a p-value, rather than a simple probability, instead of asking the
question, what is the probability of having 5 out of 10 genes with this annotation, given
that 42 out 6000 have it, we ask the question what is the probability of having 5 or more
out of 10 genes having this annotation. This is what a p-value is – the chance of seeing
your observation, or better, given the background distribution. We calculate this by
summing our probabilities for 5 out of 10, 6 out of 10, 7 out of 10 etc. Thus the
