. 2018 Jun 1;10(6):1546–1553. doi: 10.1093/gbe/evy112

Table 2.

The Details of Regression Models (supplementary table S9, Supplementary Material online) in Which the Gene’s Transformed TPM Expression Value (The Dependent Variable) Was Significantly Associated with a MEI (P < 0.01)

Model
(1) E[log₂(WBSCR17_i + 1)] = 0.432 + 1.101 * Cfa6.7_i + 0.6 * R_i + 0.374 * PC1_i – 0.099 * PC2_i^a
	Estimate	Std. Error	t Value	P-value
(Intercept)	0.432	0.163	2.655	0.0161
Locus	1.101	0.264	4.176	0.000568
RNAseq2	0.600	0.230	2.609	0.0178
PC1	0.374	0.500	0.751	0.4626
PC2	−0.099	0.468	−0.211	0.8354
(2) E[log₂ (WBSCR27_i + 1)] = 0.854 − 0.637 * Cfa6.66_i + 0.552 * R_i – 1.074 * PC1_i – 0.406 * PC2_i^a
	Estimate	Std. Error	t Value	P-value
(Intercept)	0.854	0.217	3.929	0.0010
Locus	−0.637	0.199	−3.200	0.00499
RNAseq2	0.552	0.243	2.268	0.0359
PC1	−1.074	0.555	−1.933	0.0691
PC2	−0.406	0.552	−0.736	0.4713
(3) E[log₂(RPL37_i + 1)] = 3.029 + 1.944 * Cfa6.24_i + 3.355 * R_i – 2.168 * PC1_i – 0.921 * PC2_i^a
	Estimate	Std. Error	t Value	P-value
(Intercept)	3.029	0.624	4.851	0.0001
Locus	1.944	0.456	4.262	0.000469
RNAseq2	3.355	0.488	6.880	0.000002
PC1	−2.168	1.240	−1.748	0.0975
PC2	−0.921	1.113	−0.827	0.4189
(4) E[log₂(LIMK1_i + 1)] = 0.123 + 0.420 * Cfa6.7_i + 0.153 * R_i – 0.326 * PC1_i – 0.352 * PC2_i^a
	Estimate	Std. Error	t Value	P-value
(Intercept)	0.123	0.084	1.469	0.1592
Locus	0.420	0.136	3.085	0.00638
RNAseq2	0.153	0.119	1.288	0.2141
PC1	−0.326	0.257	−1.266	0.2217
PC2	0.352	0.241	1.459	0.1617
(5) E[log₂ (BCL7B_i + 1)] = 2.218 − 0.582 * Cfa6.9_i + 0.497 * R_i + 1.077 * PC1_i – 0.916 * PC2_i^a
	Estimate	Std. Error	t Value	P-value
(Intercept)	2.218	0.350	6.345	0.00001
Locus	−0.582	0.193	−3.011	0.00751
RNAseq2	0.497	0.197	2.529	0.0210
PC1	1.077	0.399	2.697	0.0147
PC2	0.916	0.383	2.389	0.0280
(6) E[log₂(BAZ1B₂_i + 1)]^% = -0.215 + 1.44Cfa6.41_i + 0.227R_i + 1.936PC1_i – 0.996PC2_i^a
	Estimate	Std. Error	t Value	P-value
(Intercept)	−0.215	0.392	−0.548	0.5902
Locus	1.440	0.492	2.926	0.00901
RNAseq2	0.227	0.507	0.447	0.6599
PC1	1.936	1.292	1.498	0.1515
PC2	−0.996	1.099	−0.906	0.3768

NOTE.—Additional covariates were included adjust for potential confounding: two principle components (PC1 and PC2) to account for genetic structure and RNA-seq method (R) to account for batch effects. All models except model 3 (log₂(RPL37_i + 1)) demonstrate a good fit with the underlying modeling assumptions.

Equations represent the expected log₂ (TPM + 1) value for wolf i as predicted by the locus and additional coefficients.

BAZ1B_i = ENSCAFT00000046458.2.