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I am trying to understand the analysis generated by STRING. In analysis for biological processes table, there is a column titled "count in gene set." This gives a value for example "68 of 498".

Table

What does this refer to?

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It means the software has 4753 genes it has labeled with "biological regulation" and the short list you gave has 45 of those genes. That is a little higher than you might expect by chance if you'd given a random gene list of the same size.

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  • $\begingroup$ 2.94e-06 FDR suggests to me it is significantly higher than you might expect by chance. $\endgroup$ – Jonathan Moore Jun 13 at 7:28

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