Table 1.

Proteins with significant 3D (i.e., spatial) mutation clustering identified with CLUMPS

Protein	Spatial clustering			Positional clustering P
	P	$q_{\text{full}}$	$q_{\text{restricted}}$
Full analysis
PTEN*	1e-06	0.001	0.0001	8e-08
PTPN11†	1e-06	0.001	0.0001	0.0003
PIK3CA†	1e-06	0.001	0.0001	7e-08
TP53*	1e-06	0.001	0.0001	8e-08
FBXW7*	2e-05	0.02	0.002	6e-08
BRAF†	3e-05	0.02	0.002	5e-08
PPP2R1A*	6e-05	0.04	0.003	0.0003
NUF2	9e-05	0.05	—	0.4
HRAS†	0.0001	0.05	0.005	9e-08
CDKN2A*	0.0001	0.05	0.005	6e-08
Restricted analysis
SPOP*	0.001	0.4	0.04	4e-05
STK11*	0.001	0.4	0.05	0.9
EGFR†	0.001	0.5	0.05	6e-08
VHL*	0.002	0.5	0.05	1
MTOR	0.002	0.5	0.05	6e-08
RAC1†	0.002	0.5	0.06	1e-05
FGFR3†	0.003	0.6	0.07	0.02

q_full and q_restricted denote the FDR calculated in the full analysis of 4,062 human proteins represented in the PDB and in the restricted analysis of a subset of 311 previously implicated cancer proteins, respectively. Proteins in the bottom part of the table were significant in the restricted analysis but not in the full analysis. The P values in the “Positional clustering P” column were obtained with MutSig-CL (18) using mutations from the PanCancer compendium across the whole gene sequence (3).

^*Known tumor suppressor.

^†Known oncoprotein.