A Drosophila protein-interaction map centered on cell-cycle regulators

Table 2 Enrichment of the most frequently classified gene functions

Description	BD genes				AD Genes				Same-pair interactions
	Exp	Rand	P	Ratio	Exp	Rand	P	Ratio	Exp	Rand	P	Ratio
Protein modification	30	2.92	<0.00002	10.3	21	11.12	0.00210	1.9	25	14.86	0.09916	1.7
Cell cycle	22	1.27	<0.00002	17.3	19	4.83	<0.00002	3.9	26	4.40	0.00006	5.9
DNA metabolism	14	0.79	<0.00002	17.7	6	2.99	0.03006	2.0	6	1.15	0.00860	5.2
Transcription	9	2.04	0.00002	4.4	14	7.77	0.01134	1.8	7	1.85	0.00242	3.8
Gametogenesis	9	1.49	<0.00002	6.0	13	5.69	0.00172	2.3	7	1.53	0.00072	4.6
Neurogenesis	8	1.91	0.00018	4.2	12	7.29	0.03142	1.6	14	3.75	0.00168	3.7
Cell-surface receptor-linked signal transduction	8	2.48	0.00088	3.2	11	9.39	0.23272	1.2	5	3.05	0.12498	1.6
DNA repair	6	0.45	<0.00002	13.4	7	1.71	0.00030	4.1	3	0.28	0.00064	10.8
Intracellular signaling cascade	6	0.65	0.00002	9.3	6	2.44	0.01036	2.5	3	0.98	0.03602	3.1
Imaginal disk development	5	0.80	0.00022	6.3	9	3.04	0.00092	3.0	3	0.45	0.00266	6.7
Average	11.7	1.48	0.00022	9.2	11.8	5.63	0.03209	2.4	9.9	3.23	0.02769	4.71

The top 10 most frequently classified BD gene functions, derived from GO biological process level 4 (see Materials and methods), are shown. The number of proteins or pairs of proteins in our experimental data (Exp) with each GO function is shown, alongside the average number of times the function would appear in a random interaction map (Rand) having the same topology and number of proteins (see Materials and methods), and the ratio of Exp/Rand. The functions listed are significantly enriched in the BD list, to P < 0.001, and most to P < 0.0003. Cell cycle, DNA metabolism and DNA repair (highlighted) are the three most proportionally enriched classifications in the BD list, These classes are also enriched for self-associations in the interaction list, with cell cycle and DNA metabolism around six- and fivefold enriched, while DNA repair is approximately 11-fold more self-associated than expected by chance. Of these three, DNA metabolism is not significantly enriched in the AD gene list (P > 0.03), while the other two classifications are approximately fourfold enriched. A complete list of all functions and function pairs found in the interaction data is in Additional data file 4.

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