Table 3.
Number (percent) of linkages between two genes identified by the TAO-Gen algorithm in 1,000 Monte Carlo simulations of the hypothetical eight-gene network shown in Figure 3.
| From gene number | To cell number
|
||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | ||
| 100 Chips | 1 | —— | 3 (0.3) | 1,000 (100)a | 1,000 (100)a | 4 (0.4) | 1 (0.1) | 4 (0.4) | 5 (0.5) |
| 2 | 0 (0) | —— | 999 (99.9)a | 9 (0.9) | 1,000 (100)a | 1 (0.1) | 3 (0.3) | 7 (0.7) | |
| 3 | 0 (0) | 1 (0.1) | —— | 1,000 (100)a | 0 (0) | 0 (0) | 0 (0) | 1,000 (100)a | |
| 4 | 0 (0) | 0 (0) | 0 (0) | —— | 0 (0) | 0 (0) | 0 (0) | 0 (0) | |
| 5 | 0 (0) | 0 (0) | 0 (0) | 3 (0.3) | —— | 0 (0) | 1,000 (100)a | 999 (99.9)a | |
| 6 | 2 (0) | 0 (0) | 2 (0.2) | 2 (0.2) | 2 (0.2) | —— | 1,000 (100)a | 8 (0.8) | |
| 7 | 0 (0) | 0 (0) | 0 (0) | 1 (0.1) | 0 (0) | 0 (0) | —— | 1,000 (100)a | |
| 8 | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | —— | |
| 50 Chips | 1 | —— | 4 (0.4) | 980 (98)a | 1,000 (100)a | 23 (2.3) | 11 (1.1) | 23 (2.3) | 8 (0.8) |
| 2 | 8 (0.8) | —— | 977 (97.7)a | 19 (1.9) | 989 (98.9)a | 6 (0.6) | 13 (1.3) | 24 (2.4) | |
| 3 | 14 (1.4) | 2 (0.2) | —— | 995 (99.5)a | 3 (0.3) | 3 (0.3) | 9 (0.9) | 1,000 (100)a | |
| 4 | 0 (0) | 0 (0) | 5 (0.5) | —— | 0 (0) | 0 (0) | 1 (0.1) | 0 (0) | |
| 5 | 2 (0.2) | 9 (0.9) | 14 (1.4) | 7 (0.7) | —— | 4 (0.4) | 991 (99.1)a | 973 (97.3)a | |
| 6 | 10 (1) | 4 (0.4) | 15 (1.5) | 13 (1.3) | 15 (1.5) | —— | 989 (98.9)a | 11 (1.1) | |
| 7 | 1 (0.1) | 0 (0) | 0 (0) | 7 (0.7) | 7 (0.7) | 2 (0.2) | —— | 998 (99.8)a | |
| 8 | 0 (0) | 0 (0) | 0 (0) | 5 (0.5) | 0 (0) | 0 (0) | 2 (0.2) | —— | |
| 25 Chips | 1 | —— | 33 (3.3) | 832 (83.2)a | 960 (96)a | 26 (2.6) | 18 (1.8) | 26 (2.6) | 50 (5) |
| 2 | 20 (2) | —— | 751 (75.1)a | 63 (6.3) | 912 (91.2)a | 14 (1.4) | 57 (5.7) | 94 (9.4) | |
| 3 | 37 (3.7) | 46 (4.6) | —— | 933 (93.3)a | 10 (1) | 5 (0.5) | 46 (4.6) | 962 (96.2) | |
| 4 | 1 (0.1) | 0 (0) | 63 (6.3) | —— | 2 (0.2) | 0 (0) | 2 (0.2) | 11 (1.1) | |
| 5 | 5 (0.5) | 50 (5) | 59 (5.9) | 34 (3.4) | —— | 9 (0.9) | 905 (90.5)a | 811 (81.1) | |
| 6 | 9 (0.9) | 10 (1) | 19 (1.9) | 38 (3.8) | 64 (6.4) | —— | 857 (85.7)a | 69 (6.9) | |
| 7 | 2 (0.2) | 0 (0) | 21 (2.1) | 24 (2.4) | 60 (6) | 19 (1.9) | —— | 964 (96.4) | |
| 8 | 2 (0.2) | 0 (0) | 13 (1.3) | 9 (0.9) | 0 (0) | 0 (0) | 33 (3.3) | —— | |
| 10 Chips | 1 | —— | 51 (5.1) | 516 (51.6)a | 702 (70.2)a | 63 (6.3) | 30 (3) | 73 (7.3) | 141 (14.1) |
| 2 | 49 (4.9) | —— | 335 (33.5)a | 155 (15.5) | 590 (59)a | 35 (3.5) | 171 (17.1) | 166 (16.6) | |
| 3 | 73 (7.3) | 84 (8.4) | —— | 596 (59.6)a | 67 (6.7) | 16 (1.6) | 126 (12.6) | 641 (64.1)a | |
| 4 | 23 (2.3) | 15 (1.5) | 227 (22.7) | —— | 11 (1.1) | 8 (0.8) | 22 (2.2) | 71 (7.1) | |
| 5 | 16 (1.6) | 106 (10.6) | 79 (7.9) | 87 (8.7) | —— | 33 (3.3) | 519 (51.9)a | 375 (37.5)a | |
| 6 | 35 (3.5) | 30 (3) | 73 (7.3) | 93 (9.3) | 95 (9.5) | —— | 408 (40.8)a | 187 (18.7) | |
| 7 | 9 (0.9) | 18 (1.8) | 74 (7.4) | 79 (7.9) | 168 (16.8) | 51 (5.1) | —— | 693 (69.3)a | |
| 8 | 3 (0.3) | 2 (0.2) | 68 (6.8) | 51 (5.1) | 24 (2.4) | 8 (0.8) | 135 (13.5) | —— | |
a
Linkage that exists in the original simulated model.