Table 5.

Comparing the data structures to compute the goProfiles test and the one based on enrichment contingency tables.

	Non-enriched in both lists			Enriched only in list 1			Enriched only in list 2			Enriched in both lists
GO term number	1	$\cdots$	$a=n_{00}$	$a+1$	$\cdots$	$b=a+n_{10}$ $=n_{.0}$	$b+1$	$\cdots$	$c=b+n_{01}$	$c+1$	$\cdots$	$c+n_{11}$ $=n$
Annotation frequency in gene list 1	$F_{11}$	$\cdots$	$F_{1a}$	$F_{1(a+1)}$	$\cdots$	$F_{1b}$	$F_{1(b+1)}$	$\cdots$	$F_{1c}$	$F_{1(c+1)}$	$\cdots$	$F_{1n}$
Annotation frequency in gene list 2	$F_{21}$	$\cdots$	$F_{2a}$	$F_{2(a+1)}$	$\cdots$	$F_{2b}$	$F_{2(b+1)}$	$\cdots$	$F_{2c}$	$F_{2(c+1)}$	$\cdots$	$F_{2n}$
Enrichment in list 1	0	$\cdots$	0	1	$\cdots$	1	0	$\cdots$	0	1	$\cdots$	1
Enrichment in list 2	0	$\cdots$	0	0	$\cdots$	0	1	$\cdots$	1	1	$\cdots$	1

In the latter test, the annotation frequencies are substituted by 0 and 1 (i.e., “non-enriched” and “enriched” GO term.) and if the test is based on the Sorensen–Dice similarity, the first set of GO terms (non-enriched in both lists) is ignored. The GO terms are arbitrarily ordered: from left to right, first there are all those non-enriched in both lists ($n_{00}$ in total), next those enriched in the first list but not in the second one ($n_{10}$), then those enriched in the second list but not in the first ($n_{01}$) and finally those GO terms enriched in both lists ($n_{11}$)