Table 1.
Statistics from microarray analysis of down-regulated genes (< 50% of control)
| Distance (d) | 0 | 1 | 2 | 3 | ≥ 4 | Total |
|---|---|---|---|---|---|---|
| (a) gap-GR14 | ||||||
| Complementary genes (off-target candidate genes) | 8 | 440 | 5693 | 9583 | 3697 | 19,421 |
| Expressed genes | 6 | 234 | 3530 | 5935 | 1462 | 11,167 |
| Off-target genes | 6 | 168 | 1539 | 668 | 90 | 2471 |
| Percent of off-target genes | 100 | 71.8 | 43.6 | 11.3 | 6.2 | 22.1 |
| Distance (d) | 0 | 1 | 2 | 3 | 4 | ≥ 5 | Total |
|---|---|---|---|---|---|---|---|
| (b) gap-GR18-1 | |||||||
| Complementary genes (off-target candidate genes) | 1 | 0 | 52 | 1432 | 7833 | 10,103 | 19,421 |
| Expressed genes | 1 | 0 | 25 | 850 | 4860 | 5363 | 11,099 |
| Off-target genes | 1 | 0 | 11 | 146 | 259 | 65 | 482 |
| Percent of off-target genes | 100 | NA | 44.0 | 17.2 | 5.3 | 1.2 | 4.3 |
| (c) gap-GR18-2 | |||||||
| Complementary genes (off-target candidate genes) | 1 | 0 | 44 | 1153 | 7567 | 10,656 | 19,421 |
| Expressed genes | 1 | 0 | 22 | 677 | 4677 | 5709 | 11,086 |
| Off-target genes | 1 | 0 | 17 | 329 | 1204 | 430 | 1981 |
| Percent of off-target genes | 100 | NA | 77.3 | 48.6 | 25.7 | 7.5 | 17.9 |
| (d) gap-GR18-3 | |||||||
| Complementary genes (off-target candidate genes) | 1 | 1 | 73 | 1595 | 7805 | 9946 | 19,421 |
| Expressed genes | 1 | 0 | 42 | 947 | 5029 | 5102 | 11,121 |
| Off-target genes | 1 | 0 | 26 | 228 | 311 | 64 | 630 |
| Percent of off-target genes | 100 | NA | 61.9 | 24.1 | 6.2 | 1.3 | 5.7 |
Statistics from microarray analysis of the cells treated with (a) gap-GR14, (b) gap-GR18-1, (c) gap-GR18-2, and (d) gap-GR18-3 ASO. Complementary genes: The number of off-target candidate genes identified by in silico analysis. Expressed genes: The number of “Complementary genes” that are on a microarray and were expressed in Huh-7 cells. Genes with sufficient hybridization signals to be called “present” in at least three of four trials were used in this study. Off-target genes: The number of “Expressed genes” in which gene expression was significantly down-regulated to less than 50% of the level in the control group. Percent of off-target genes: The proportion of genes in “Off-target genes” that were in “Expressed genes.” Note that “Off-target genes” in each d = 0 group included the on-target gene (GR) itself