Table 1.

Significant genes with mutation cluster associations

Cancer type	Gene	Cluster index	Position (AA) a	Number of samples	Wilcoxon b	Regression-based test c
					P	Model p	t value	Pr(>|t|)
LAML	CEBPA	7	300::310	6	1.14 × 10−4	8.75 × 10−6	4.599	8.75 × 10−6
LAML	DNMT3A	17	882	21	0.018	7.98 × 10−3	−2.691	7.98 × 10−3
LAML	RUNX1	6	171:174	6	0.042	0.019	1.994	0.048
LAML	FLT3	2	593::604	28	0.041	0.020	2.180	0.031
LAML	FLT3	4	835:839	12	0.035	0.020	2.072	0.040
BLCA	NFE2L2	1	24::34	6	4.48 × 10−4	3.96 × 10−5	4.328	3.96 × 10−5
BLCA	KDM6A	10	555	5	0.035	0.013	−2.557	0.013
BLCA	FGFR3	4	248:249	5	3.26 × 10−3	0.017	2.430	0.017
BRCA	GATA3	4	329::335	10	7.37 × 10−5	1.86 × 10−5	2.914	3.67 × 10−3
BRCA	GATA3	5	345::365	10	1.45 × 10−3	1.86 × 10−5	2.038	0.042
BRCA	GATA3	7	395::410	17	7.33 × 10−5	1.86 × 10−5	2.806	5.16 × 10−3
BRCA	GATA3	8	419::445	16	1.23 × 10−3	1.86 × 10−5	2.766	5.82 × 10−3
BRCA	PIK3R1	3	455::465	6	0.136	7.74 × 10−4	2.045	0.041
BRCA	PIK3R1	5	559::577	9	2.76 × 10−3	7.74 × 10−4	3.228	1.30 × 10−3
COADREAD	TP53	9	194:195:196	6	1.04 × 10−3	1.63 × 10−6	−4.423	1.74 × 10−5
COADREAD	TP53	10	207:212:213	6	2.18 × 10−3	1.63 × 10−6	−4.514	1.19 × 10−5
COADREAD	APC	3	213:216	11	8.10 × 10−5	4.00 × 10−4	−4.318	3.13 × 10−5
COADREAD	APC	16	564:567	6	0.093	4.00 × 10−4	−2.688	8.14 × 10−3
COADREAD	TGFBR2	1	125	13	1.28 × 10−3	9.29 × 10−4	−3.362	9.29 × 10−4
COADREAD	MSH3	2	381	9	0.017	0.012	−2.543	0.012
GBM	EGFR	9	289	15	4.46 × 10−4	1.84 × 10−4	3.490	6.73 × 10−4
GBM	EGFR	14	596:598	14	4.29 × 10−3	1.84 × 10−4	2.691	8.13 × 10−3
GBM	IDH1	1	132	8	4.62 × 10−4	5.46 × 10−4	−3.537	5.46 × 10−4
HNSC	TP53	7	98::110	9	0.05	3.28 × 10−6	−2.509	0.013
HNSC	TP53	13	265::286	42	0.264	3.28 × 10−6	2.120	0.035
HNSC	TP53	14	292::306	10	6.78 × 10−5	3.28 × 10−6	−4.595	6.64 × 10−6
HNSC	HRAS	1	11:12:13	9	1.09 × 10−3	7.61 × 10−6	4.558	7.61 × 10−6
KIRC	VHL	2	39::45	5	0.814	9.33 × 10−3	−2.143	0.033
KIRC	VHL	3	60::137	123	0.019	9.33 × 10−3	2.278	0.023
KIRC	VHL	4	143::189	62	0.053	9.33 × 10−3	2.430	0.016
LUAD	KRAS	1	12:13	43	3.18 × 10−7	2.21 × 10−6	4.911	2.21 × 10−6
LUAD	EGFR	4	746:751:754	7	2.24 × 10−4	4.16 × 10−5	4.436	1.70 × 10−5
LUSC	TP53	10	151::163	19	9.77 × 10−4	1.11 × 10−5	3.559	5.05 × 10−4
LUSC	TP53	11	172::183	13	4.56 × 10−4	1.11 × 10−5	3.910	1.42 × 10−4
LUSC	TP53	12	193:195:196	6	0.044	1.11 × 10−5	2.158	0.033
LUSC	TP53	14	234::252	24	4.62 × 10−5	1.11 × 10−5	4.433	1.84 × 10−5
LUSC	TP53	15	259::287	27	2.63 × 10−3	1.11 × 10−5	3.458	7.16 × 10−4
UCEC	PTEN	12	165::182	8	0.050	2.39 × 10−4	1.981	0.049
UCEC	PTEN	15	233:237:240	12	8.48 × 10−4	2.39 × 10−4	−3.678	3.04 × 10−4
UCEC	PTEN	20	335::344	8	1.25 × 10−3	2.39 × 10−4	3.252	1.35 × 10−3
UCEC	PIK3R1	8	442::466	18	0.012	8.75 × 10−4	2.493	0.013
UCEC	PIK3R1	12	558:593	33	1.68 × 10−3	8.75 × 10−4	3.108	2.16 × 10−3
UCEC	LIMCH1	3	421	6	6.25 × 10−3	3.62 × 10−3	−2.943	3.62 × 10−3
UCEC	RPL22	1	16	23	2.19 × 10−3	8.61 × 10−3	−2.652	8.61 × 10−3

^aTwo continuous colons (::) indicate that there are multiple positions with mutations. AA: amino acid position.

^bWilcoxon test was performed in the comparison of the samples having a single cluster with the wild type samples.

^cRegression-based test was performed using all eligible clusters.