Table 2.

Top breast cancer GWAS gene hits for competing methods compared to principal angles in the 1:K setting. Though ${\beta }^{\left(S\right)}$ is unknown, we use ${\hat{\beta }}^{\left(S\right)}$ as an estimate of ${\beta }^{\left(S\right)}$. The angle between ${\hat{\beta }}^{\left(S\right)}$ and $u_k^{\left(S\right)}$ is ${\hat{\theta }}_k^{\left(S\right)}$. The top 15 most significant genes, as determined by the smallest of the p-values of the four methods (first and last PCs, VC and MinP), are listed and sorted in increasing order by their ${\theta }_1^{\left(S\right)}$

Gene	K	MinP pval	$V_1^{\left(S\right)}\text{ pval}$	$V_K^{\left(S\right)}\text{ pval}$	$Q^{\left(S\right)}\text{ pval}$	${\hat{\theta }}_1^{\left(S\right)}$	${\hat{\theta }}_K^{\left(S\right)}$
STXBP1	9	4.00E-04	1.52E-04	9.25E-02	1.52E-03	6.3	88.9
PTCD3	12	2.66E-04	4.36E-05	8.45E-01	1.13E-04	7.7	89.9
POLR1A	16	4.00E-04	6.37E-05	1.54E-01	3.43E-04	9.0	90.0
TBK1	11	1.28E-03	3.59E-05	2.24E-01	5.44E-05	10.8	89.1
C11orf49	24	2.57E-03	3.11E-04	8.50E-01	3.84E-04	11.5	90.0
VAPB	25	7.53E-03	2.50E-04	1.34E-02	4.93E-04	15.7	89.8
XPOT	9	1.07E-03	2.04E-04	9.45E-02	1.59E-04	17.1	89.3
C1orf71	25	1.65E-02	1.19E-04	8.37E-01	6.40E-04	18.4	89.9
CNGA3	26	1.19E-03	1.33E-04	5.22E-01	1.36E-04	28.4	89.9
FGFR2	35	1.00E-04	8.15E-05	1.32E-01	3.88E-05	28.9	89.3
TMEM175	10	5.00E-04	5.05E-03	2.87E-04	2.96E-03	32.9	88.4
ZNF19	6	3.71E-02	4.55E-02	2.12E-04	3.54E-04	36.5	86.1
VWA3B	51	1.39E-03	1.23E-03	2.82E-01	2.10E-04	39.3	90.0
DACT1	9	1.26E-01	1.59E-01	1.55E-04	1.32E-01	44.9	75.6
DGKQ	9	3.31E-04	5.01E-01	1.22E-05	7.33E-03	80.1	87.0