TABLE IV.

Associations detected in the gemcitabine study using the Bayesian integrative model or the all-APCA approaches. Results from different prior model specifications for p_a and p_b are presented for the Bayesian integrative model. Effects determined to be significant at the 0.05 level from the APCA (after adjustment for multiple testing) are included with bolded P-values. For the Bayesian integrative model, genomic variables are included if (1) the 95% credible interval for the direct mRNA expression effects did not contain zero; (2) the P(γ_jk | data) ≥ 0.25 with the Beta prior for the indirect SNP effect; or (3) the P(φ_k| data) ≥ 0.15 with Beta prior for the direct SNP effect

Effect type	mRNA gene expression variation	Genetic variation	APCA p-value	p ~ Beta posterior probability or 95% CI	p ~ Uniform posterior probability or 95% CI	p = 0.2 posterior probability or 95% CI
SNP—mRNA association or indirect SNP effect	SLC28A1	CMPK1	4.94e–4	0.35	0.22	0.65
	SLC28A2	NT5C1B	5.77e–3	0.25	0.13	0.53
	CMPK1	CMPK1	4.06e–4	0.37	0.20	0.70
	CDA	RRM2	3.97e–3	0.28	0.17	0.51
	NT5C3L	NT5C3L	1.42e–18	1.00	1.00	1.00
mRNA expression-—IC50 association or direct mRNA effect	SLC29A1	—	2.79e–3	(−0.225, 0.066)	(−0.225, 0.065)	(−0.226, 0.067)
	DCK	—	2.65e–3	(−0.266, −0.004)	(−0.267, −0.003)	(−0.267, −0.003)
	NT5C3	—	9.75e–6	(0.035, 0.266)	(0.034, 0.266)	(0.035, 0.267)