Table s13. Result of the core-periphery structure analysis. The consistency for a clusters and GO terms to remain in the same core-periphery substructure across different cutoffs was measured across six cutoff levels of annotation significance (i.e., p < 0.01, 0.005, 0.001, 5x10-4, 1x10-5, and 5x10-5). Large portions of the clusters in all datasets remain in the same core-periphery substructures at all different cutoffs (64% for ABGM, 57% for HCDC, 46% for YCDC and 45% for YHS). For example, 23 among 36 clusters remain in the same substructures, though the cutoff level is different, and among them 2 in the core, 4 in the peripheral, and 17 clusters remain in the independent substructure for AGBM dataset. (co: core substructure; cm: communicating substructure; pr: peripheral substructure; in: independent substructure).
|
consistency |
for clusters |
for GO terms |
|||||
|
count |
count (co, cm, pr, in) |
|
count |
count (co, cm, pr, in) |
|
||
|
AGBM |
no change |
23 |
(2, 0, 4, 17) |
|
78 |
(29, 9, 12, 28) |
|
|
2 |
11 |
(1, 1, 9, 11) |
|
32 |
(3, 9, 26, 26) |
|
|
|
3 |
2 |
(1, 2, 1, 2) |
|
12 |
(7, 12, 6, 11) |
|
|
|
4 |
0 |
(0, 0, 0, 0) |
|
0 |
(0, 0, 0, 0) |
|
|
|
HCDC |
no change |
42 |
(1, 3, 16, 22) |
|
192 |
(0, 39, 84, 69) |
|
|
2 |
24 |
(4, 7, 18, 19) |
|
132 |
(15, 64, 112, 73) |
|
|
|
3 |
6 |
(1, 6, 6, 5) |
|
31 |
(12, 31, 31, 19) |
|
|
|
4 |
2 |
(2, 2, 2, 2) |
|
1 |
(1, 1, 1, 1) |
|
|
|
YCDC |
no change |
35 |
(1, 4, 21, 9) |
|
200 |
(23, 57, 103, 17) |
|
|
2 |
34 |
(9, 12, 29, 18) |
|
130 |
(21, 89, 120, 30) |
|
|
|
3 |
7 |
(4, 7, 7, 3) |
|
50 |
(39, 50, 50, 11) |
|
|
|
4 |
0 |
(0, 0, 0, 0) |
|
1 |
(1, 1, 1, 1) |
|
|
|
YHS |
no change |
36 |
(1, 1, 19, 15) |
|
224 |
(0, 31, 153, 40) |
|
|
2 |
32 |
(3, 5, 30, 26) |
|
114 |
(5, 59, 110, 54) |
|
|
|
3 |
12 |
(9, 12, 12, 3) |
|
33 |
(27, 33, 33, 6) |
|
|
|
4 |
0 |
(0, 0, 0, 0) |
|
0 |
(0, 0, 0, 0) |
|
|