Table 4.

Significant genes and proteins in the WNT signalling pathway from TCGA legacy datasets. (A) List of significant genes and their associated hazard ratio, p-value, and mafdr (estimate positive false discovery rate for multiple hypothesis testing). Hazard ratios smaller than one (between 0 and 1) indicate a negative association (decreased risk), hazard ratios of >1 indicate a positive association (increased risk). The last column, proteomics, indicates whether proteomics data for this gene were available. If yes, a Y is depicted. (B) List of significant proteins and their associated hazard ratio, p-value, and mafdr. Significant features highlighted in blue were found in published mechanistic models of the WNT pathway [27,28,29,30,31,32].

A	Genes	Hazard Ratio	p-Value	mafdr	Patient	Proteomics
1	DVL3	2.8158	2.58$\times {10}^{-4}$	1.37$\times {10}^{-2}$	329
2	VANGL2	2.7693	1.08$\times {10}^{-3}$	1.40$\times {10}^{-2}$	329
3	WNT6	2.3175	1.34$\times {10}^{-3}$	1.40$\times {10}^{-2}$	299
4	TCF7L1	2.0324	1.35$\times {10}^{-3}$	1.40$\times {10}^{-2}$	329
5	CER1	2.8871	1.42$\times {10}^{-3}$	1.40$\times {10}^{-2}$	147
6	SOX17	2.1048	1.59$\times {10}^{-3}$	1.40$\times {10}^{-2}$	329
7	NKD2	2.8598	1.85$\times {10}^{-3}$	1.40$\times {10}^{-2}$	329
8	DKK1	1.9732	2.16$\times {10}^{-3}$	1.43$\times {10}^{-2}$	309
9	SFRP2	1.8539	3.94$\times {10}^{-3}$	2.09$\times {10}^{-2}$	327	Y
10	PLCB1	2.9436	4.32$\times {10}^{-3}$	2.09$\times {10}^{-2}$	329
11	PRICKLE1	1.8229	5.01$\times {10}^{-3}$	2.09$\times {10}^{-2}$	329
12	MAPK8	0.5491	5.19$\times {10}^{-3}$	2.09$\times {10}^{-2}$	329	Y
13	PRICKLE2	1.8104	5.38$\times {10}^{-3}$	2.09$\times {10}^{-2}$	329
14	MYC	0.5535	5.53$\times {10}^{-3}$	2.09$\times {10}^{-2}$	329
15	WIF1	2.4639	6.46$\times {10}^{-3}$	2.20$\times {10}^{-2}$	246
16	CAMK2B	1.9981	6.66$\times {10}^{-3}$	2.20$\times {10}^{-2}$	302
17	WNT3A	2.3137	7.09$\times {10}^{-3}$	2.21$\times {10}^{-2}$	243
18	LEF1	1.9751	8.65$\times {10}^{-3}$	2.52$\times {10}^{-2}$	329
19	RHOA	0.4792	9.47$\times {10}^{-3}$	2.52$\times {10}^{-2}$	329	Y
20	MAPK10	1.7294	9.88$\times {10}^{-3}$	2.52$\times {10}^{-2}$	329
21	CAMK2D	0.5514	1.05$\times {10}^{-2}$	2.52$\times {10}^{-2}$	329	Y
22	WNT3	1.8141	1.06$\times {10}^{-2}$	2.52$\times {10}^{-2}$	328
23	FZD8	1.8913	1.09$\times {10}^{-2}$	2.52$\times {10}^{-2}$	329
24	SERPINF1	1.7116	1.14$\times {10}^{-2}$	2.52$\times {10}^{-2}$	329	Y
25	FZD1	1.7251	1.24$\times {10}^{-2}$	2.55$\times {10}^{-2}$	329
26	NKD1	1.8480	1.25$\times {10}^{-2}$	2.55$\times {10}^{-2}$	329
27	CXXC4	1.8290	2.62$\times {10}^{-2}$	1.34$\times {10}^{-2}$	318
28	PPP3CA	0.4335	2.62$\times {10}^{-2}$	1.39$\times {10}^{-2}$	329	Y
29	PLCB3	0.5772	2.74$\times {10}^{-2}$	1.50$\times {10}^{-2}$	329
30	CSNK1A1L	0.4710	2.74$\times {10}^{-2}$	1.55$\times {10}^{-2}$	321
31	PLCB2	1.6955	3.46$\times {10}^{-2}$	2.10$\times {10}^{-2}$	329
32	ROR2	1.6511	3.46$\times {10}^{-2}$	2.14$\times {10}^{-2}$	329
33	PRKCB	0.5888	3.46$\times {10}^{-2}$	2.15$\times {10}^{-2}$	329
34	WNT2	0.5479	3.52$\times {10}^{-2}$	2.26$\times {10}^{-2}$	329
35	SFRP1	1.6386	3.53$\times {10}^{-2}$	2.33$\times {10}^{-2}$	322
36	WNT10A	2.1170	3.69$\times {10}^{-2}$	2.56$\times {10}^{-2}$	328
37	GSK3B	1.6397	3.69$\times {10}^{-2}$	2.61$\times {10}^{-2}$	329	Y
38	FRAT1	0.6144	3.69$\times {10}^{-2}$	2.65$\times {10}^{-2}$	329
39	SENP2	2.2535	3.84$\times {10}^{-2}$	2.92$\times {10}^{-2}$	329
40	DKK4	1.7497	3.84$\times {10}^{-2}$	2.96$\times {10}^{-2}$	301
41	CTNNBIP1	1.5838	3.84$\times {10}^{-2}$	2.97$\times {10}^{-2}$	329
42	FZD7	2.0424	4.18$\times {10}^{-2}$	3.40$\times {10}^{-2}$	329
43	WNT1	1.7533	4.18$\times {10}^{-2}$	3.46$\times {10}^{-2}$	244
44	DKK2	1.8152	4.18$\times {10}^{-2}$	3.59$\times {10}^{-2}$	326
45	WNT16	2.0367	4.18$\times {10}^{-2}$	3.62$\times {10}^{-2}$	276
46	WNT2B	0.6417	4.18$\times {10}^{-2}$	3.68$\times {10}^{-2}$	329
47	NFATC4	1.5715	4.18$\times {10}^{-2}$	3.70$\times {10}^{-2}$	329
48	NLK	1.7784	4.23$\times {10}^{-2}$	3.83$\times {10}^{-2}$	329
49	NOTUM	1.5754	4.34$\times {10}^{-2}$	4.08$\times {10}^{-2}$	329
50	CSNK2A3	0.4868	4.34$\times {10}^{-2}$	4.09$\times {10}^{-2}$	329
51	WNT4	0.6060	4.82$\times {10}^{-2}$	4.64$\times {10}^{-2}$	329
52	FZD5	0.6579	4.82$\times {10}^{-2}$	4.81$\times {10}^{-2}$	329
53	DAAM1	1.7076	4.82$\times {10}^{-2}$	4.82$\times {10}^{-2}$	329
B	Proteins	Hazard Ratio	p -Value	mafdr	Patient
1	PRKCA	0.1557	1.62$\times {10}^{-3}$	3.66$\times {10}^{-3}$	63
2	ROCK2	5.7810	1.78$\times {10}^{-3}$	3.66$\times {10}^{-3}$	71
3	CSNK2A1	5.6824	1.83$\times {10}^{-3}$	3.66$\times {10}^{-3}$	73
4	LRP1	0.2594	2.62$\times {10}^{-2}$	3.93$\times {10}^{-2}$	72
5	CSNK1A1	0.2846	3.71$\times {10}^{-2}$	4.46$\times {10}^{-2}$	72
6	GPC4	0.2512	4.58$\times {10}^{-2}$	4.58$\times {10}^{-2}$	50