Table 1.

Across experiment comparison of protein subsets associated with systematic error

	Not in Krogan et al. [11]	In Krogan et al. [11]
Not in Gavin et al. [10]	624	63
In Gavin et al. [10]	31	12
	P = 6.5 × 10-4	Odds ratio = 3.82

This table compares the proteins affected by a reciprocity artifact from the datasets of Gavin and coworkers [10] and Krogan and colleagues [11]. Binomial tests were applied to identify the affected protein sets within each experiment, and their overlap was assessed in the 2 × 2 contingency table. In this table, the binomial tests were applied to the two experimental datasets independently, and only those proteins in which the in-degree is much larger than the out-degree are considered. Shown P value and odds ratio were calculated from the 2 × 2 table using the hypergeometric distribution.