Table 2. Overlap between ASD gene sets and FMRP targets.

Gene set	Number of genes	Expected : observed	P-value
Network genes	159	17.3 : 48 (1 : 2.78)	3×10−11
Truncating SNV genes	108	11.7 : 25 (1 : 2.13)	0.0003
Network non-truncating-SNV genes	138	15.0 : 40 (1 : 2.67)	4×10−9
Neuronal signaling/cytoskeleton cluster genes	69	7.49 : 15 (1 : 2.00)	0.01
Chromatin modification/regulation cluster genes	50	5.43 : 17 (1 : 3.13)	1×10−5
Postsynaptic density cluster genes	11	1.19 : 5 (1 : 4.19)	0.004
Channel activity cluster genes	21	2.28 : 9 (1 : 3.95)	0.0002
Non-network SNV genes	449	48.8 : 40 (1 : 0.82)	0.2
Sibling SNV genes	355	38.6 : 47 (1 : 1.22)	0.15

The expected and observed number of fragile X mental retardation protein (FMRP) targets²⁶ among different sets of implicated genes. The expected numbers of FMRP targets were obtained based on the proportion of rare synonymous variants observed in a recent large-scale survey of human genetic variation²⁹. The observed and expected overlaps based on another recent study of FMRP targets by Ascano et al.³⁰ are given in Supplementary Table S5. The significances of the overlaps were established using the two-tail binomial test.