Table 2.

The miR-29 family is differentially expressed between patients with normal levels versus those with extremely high levels of serum AFP

	Raw Intensity Valueb
miRNA Probea	AFP >2000ng/ulc	AFP <20ng/uld	Fold Change	Parametric p-value	FDR	Chromosome Location	Gain (%)e	Loss (%)e
miR-29a (1)	1230.14	2193.45	0.56	< 0.00001	0.0001	7q32	6.6	1.3 – 2.6
miR-29a (2)	1542.24	2730.72	0.56	< 0.00001	0.0004	7q32	6.6	1.3 – 2.6
miR-29b-2	1756	3106.81	0.57	< 0.00001	0.0001	1q32	34.2	1.3
miR-29b-1 (1)	1477.04	2545.82	0.58	< 0.00001	0.0004	7q32	6.6	1.3 – 2.6
miR-122a (1)	16063.12	27088.34	0.59	< 0.00001	0.0059	18q21	0	6.6
miR-29b-1 (2)	1377.04	2242.49	0.61	< 0.00001	0.0100	7q32	6.6	1.3 – 2.6
miR-29b-1 (2)	960.32	1559.23	0.62	< 0.00001	0.0040	7q32	6.6	1.3 – 2.6
miR-29c	1418.1	2247.65	0.63	< 0.00001	0.0059	1q32	34.2	1.3
miR-125b-1 (1)	1613.31	2482.49	0.65	0.00110	0.0328	11q24	1.3	6.6
miR-125b-1 (2)	1448.15	2194.68	0.66	0.00120	0.0315	11q24	1.3	6.6
miR-122a (2)	29564.15	40839.46	0.72	0.00070	0.0250	18q21	0	6.6
miR-let-7d	1116.67	1429.47	0.78	0.00030	0.0233	9q22	2.6	13.2
miR-let-7f	679.58	862.59	0.79	0.00060	0.0250	9q22	2.6	13.2
miR-181b-2 (1)	2216.1	1622.01	1.37	0.00010	0.0059	9q33	5.3	10.5
miR-181c	1279.19	930.72	1.37	0.00010	0.0093	19q13	9.2 – 10.5	3.9
miR-181b-1	1807.52	1193.32	1.51	0.00010	0.0044	1q32	34.2	1.3
miR-181b-2 (2)	2289.77	1470.03	1.56	< 0.00001	0.0001	9q33	5.3	10.5
miR-32	1891.71	1143.94	1.65	0.00010	0.0059	9q31	2.6	13.2

^aThe miRNA array includes multiple spots for some miRNAs therefore there are multiple probe readouts. Additional probes for miRNAs are numbered in parenthesis after the probe name.

^bMean values for miRNA expression are shown for AFP high and normal cases and were used to calculate fold change.

^cHigh AFP, n=40

^dLow AFP, n=74

^ePercent gain and loss were estimated by copy-number variation (CNV) data from 36 HCC tumor tissue samples. In cases where the miRNA is not in a gene, the genes upstream and downstream of the miRNA were used to estimate CNV.