Additional data file 10.
(a) Significant kappa scores (≥0.35 based on randomization study in Figure 3) can be obtained only for gene-gene pairs with higher overlapped annotation terms (≥10). Thus, there is no reason to calculate kappa scores, in an attempt to save the calculating time for DAVID Functional Classification, for the large number of those gene-gene pairs with fewer annotation terms overlapped. A conservative default filter is 4. (b) Such a default filer (blue curve) has somewhat greater impact on the significant kappa scores in the higher end, compared to those in the lower end. However, it will skip a significant amount of kappa calculation of gene-gene pairs.
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Huang et al. Genome Biology 2007 8:R183 doi:10.1186/gb-2007-8-9-r183