Table 2.

Autophagy gene expression profiling regulated with arsenic exposure while fed with HFD or LFD with 1 fold alteration (up- or downregulated) by PCR array.

Symbol	AVG ΔCt (Ct(GOI) − Ave Ct (HKG))				$2^{-\mathbf{\Delta }\mathbf{C}\mathbf{T}}$ *				Fold Change**			Fold Up- or Down-Regulation***
	LFD50	HFD	HFD50	LFD	LFD50	HFD	HFD50	LFD	LFD50/LFD	HFD/ LFD	HFD50/ LFD	LFD50/ LFD	HFD/ LFD	HFD50/LFD
Atg12	4.92	6.06	4.15	6.73	3.3E − 02	1.5E − 02	5.6E − 02	9.5E − 03	3.49	1.59	5.96	3.49	1.59	5.96
Atg16l1	2.25	4.41	0.76	3.92	2.1E − 01	4.7E − 02	5.9E − 01	6.6E − 02	3.17	0.71	8.91	3.17	−1.41	8.91
Atg16l2	4.92	8.68	4.10	4.74	3.3E − 02	2.4E − 03	5.8E − 02	3.8E − 02	0.88	0.07	1.55	−1.14	−15.37	1.55
Atg3	4.92	5.08	2.15	3.68	3.3E − 02	3.0E − 02	2.3E − 01	7.8E − 02	0.42	0.38	2.88	−2.37	−2.64	2.88
Atg4b	4.18	5.26	3.02	6.95	5.5E − 02	2.6E − 02	1.2E − 01	8.1E − 03	6.79	3.22	15.19	6.79	3.22	15.19
Atg4c	3.20	6.53	1.41	4.35	1.1E − 01	1.1E − 02	3.8E − 01	4.9E − 02	2.21	0.22	7.65	2.21	−4.54	7.65
Atg5	3.08	4.50	2.11	3.48	1.2E − 01	4.4E − 02	2.3E − 01	9.0E − 02	1.31	0.49	2.58	1.31	−2.03	2.58
Atg7	4.15	7.79	4.15	5.99	5.6E − 02	4.5E − 03	5.6E − 02	1.6E − 02	3.57	0.29	3.57	3.57	−3.49	3.57
Atg9a	4.92	8.68	4.15	6.88	3.3E − 02	2.4E − 03	5.6E − 02	8.5E − 03	3.87	0.29	6.61	3.87	−3.49	6.61
Becn1	4.92	5.96	4.15	6.95	3.3E − 02	1.6E − 02	5.6E − 02	8.1E − 03	4.06	1.98	6.94	4.06	1.98	6.94
Gabarap	1.24	0.96	0.56	3.16	4.2E − 01	5.1E − 01	6.8E − 01	1.1E − 01	3.76	4.59	6.04	3.76	4.59	6.04
Gabarapl1	−0.20	0.98	−0.95	−0.16	1.1E + 00	5.1E − 01	1.9E + 00	1.1E + 00	1.03	0.46	1.74	1.03	−2.19	1.74
Gabarapl2	3.90	4.84	2.43	4.19	6.7E − 02	3.5E − 02	1.9E − 01	5.5E − 02	1.22	0.64	3.38	1.22	−1.57	3.38
Hdac6	4.92	6.36	4.15	5.91	3.3E − 02	1.2E − 02	5.6E − 02	1.7E − 02	1.98	0.73	3.38	1.98	−1.37	3.38
Hsp90aa1	2.07	1.80	0.05	3.97	2.4E − 01	2.9E − 01	9.7E − 01	6.4E − 02	3.71	4.49	15.08	3.71	4.49	15.08
Hspa8	−2.31	−1.37	−3.34	−0.38	5.0E + 00	2.6E + 00	1.0E + 01	1.3E + 00	3.82	2.00	7.81	3.82	2.00	7.81
Lamp1	2.92	1.55	1.52	2.55	1.3E − 01	3.4E − 01	3.5E − 01	1.7E − 01	0.77	2.00	2.03	−1.30	2.00	2.03
Map1lc3a	4.15	5.98	4.15	6.12	5.6E − 02	1.6E − 02	5.6E − 02	1.4E − 02	3.90	1.10	3.90	3.90	1.10	3.90
Npc1	4.92	4.86	4.08	4.53	3.3E − 02	3.4E − 02	5.9E − 02	4.3E − 02	0.76	0.79	1.36	−1.32	−1.26	1.36
Ulk1	4.86	7.39	4.15	4.75	3.4E − 02	6.0E − 03	5.6E − 02	3.7E − 02	0.92	0.16	1.51	−1.08	−6.24	1.51
Wipi1	4.75	6.35	2.84	5.03	3.7E − 02	1.2E − 02	1.4E − 01	3.1E − 02	1.21	0.40	4.55	1.21	−2.50	4.55

*$2^{-\mathrm{\Delta }\text{CT}}$ (normalized gene expression) is the expression levels of gene of interest (GOI) divided the expression levels of HKG genes.

$\frac{2^{-\mathrm{CT}\left(\mathrm{GOI}\right)}}{2^{-\mathrm{CT}\left(\mathrm{HKG}\right)}}=2^{-\left[\mathrm{CT}\left(\mathrm{GOI}\right)-\mathrm{CT}\left(\mathrm{HKG}\right)\right]}=2^{-\mathrm{\Delta }\text{CT}}$.

**Fold-Change ($2^{-\mathrm{\Delta }\mathrm{\Delta }\text{CT}}$) is the normalized gene expression ($2^{-\mathrm{\Delta }\text{CT}}$) in the Test Sample divided the normalized gene expression ($2^{-\mathrm{\Delta }\text{CT}}$) in the Control Sample.

$\frac{2^{-\mathrm{\Delta }\text{CT}\left(\mathrm{expt}\right)}}{2^{-\mathrm{\Delta }\text{CT}\left(\mathrm{ctrl}\right)}}=2^{-\mathrm{\Delta }\mathrm{\Delta }\text{CT}}$ where ΔΔCT is equal to ΔCT (expt) − ΔCT (ctrl).

***Fold-Regulation represents fold-change results in a biologically meaningful way.

Fold-change values greater than one indicate a positive- or an up-regulation, and the fold-regulation is equal to the fold-change. Fold-change values less than one indicate a negative or down-regulation, and the fold-regulation is the negative inverse of the fold-change. Fold-change and fold-regulation values greater than 2 are indicated in bold; fold-change values less than 0.5 and fold-regulation values less than −2 are indicated in italic.