Skip to main content

Table 1 K90 GIL Collection Overview

From: Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study

GILA Arrays Datasets Nodes Edges <k> RMT γ ModulesB GOc Interpro KEGGC AraCycc POC GILA Arrays Datasets Nodes Edges <k> RMT γ ModulesB GOc Interpro KEGGC AraCycc POC
1 48 7 2,563 7,051 5.50 0.929 1.99 616/294 153/225 192/112 192/112 19/18 21/13 46 116 28 n.a. n.a. n.a. n.a. n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a.
2 38 2 1,921 7,807 8.13 0.943 1.85 418/226 98/135 84/50 84/50 14/19 11/34 47 105 12 1,445 4,969 6.88 0.910 1.85 280/282 122/123 119/110 54/90 15/15 10/19
3 76 22 2,919 6,415 4.40 0.844 2.13 763/251 313/219 298/130 298/130 28/20 45/36 48 269 31 2,638 11,228 8.51 0.803 1.78 489/493 316/663 231/317 103/200 35/38 45/62
4 72 12 2,764 6,565 4.75 0.872 2.07 713/319 334/448 303/168 303/168 38/17 45/23 49 39 2 1,954 9,688 9.92 0.935 1.76 413/376 177/286 160/133 78/86 15/10 14/3
5 40 2 997 4,346 8.72 0.936 1.86 197/136 115/107 81/35 81/35 11/7 3/2 50 113 27 3,520 11,996 6.82 0.809 1.92 770/497 330/350 284/222 144/99 30/5 21/14
6 123 25 2,446 15,547 12.71 0.835 1.75 507/458 254/854 203/360 203/360 24/19 18/24 51 45 9 2,377 4,570 3.85 0.911 2.20 651/223 153/132 173/75 90/43 16/9 4/3
7 75 22 2,491 4,259 3.42 0.842 2.26 705/229 267/148 251/77 251/77 21/13 10/8 52 8 1 n.a. n.a. n.a. n.a. n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a.
8 42 4 1,596 5,282 6.62 0.964 1.92 315/217 90/72 88/65 88/65 13/13 19/15 53 143 32 1,898 5,518 5.81 0.826 1.96 438/232 231/186 192/94 86/64 17/15 19/12
9 84 2 1,859 16,072 17.29 0.876 1.64 327/374 121/927 90/165 90/165 22/92 24/39 54 85 13 1,983 3,849 3.88 0.859 2.23 522/206 166/80 191/52 70/36 22/14 18/9
10 147 16 1,804 9,878 10.95 0.898 1.70 317/329 168/543 111/98 111/98 16/44 46/93 55 87 29 3,811 16,013 8.40 0.802 1.83 815/668 373/580 311/261 137/170 38/27 28/14
11 63 1 1,971 16,547 16.79 0.889 1.62 351/484 175/1070 148/402 148/402 19/39 15/46 56 40 4 1,414 13,540 19.15 0.965 1.54 206/448 87/540 63/87 23/103 8/3 46/265
12 124 14 1,257 5,985 9.52 0.875 1.75 212/294 63/93 47/43 47/43 5/16 12/8 57 27 3 1,944 7,628 7.85 0.916 1.91 506/229 106/319 125/65 52/81 13/17 32/36
13 49 5 1,293 3,808 5.89 0.952 1.96 295/158 59/84 79/39 79/39 7/16 1/2 58 131 17 1,861 8,262 8.88 0.865 1.81 367/360 283/694 183/200 79/186 38/84 33/73
14 87 10 3,286 37,336 22.72 0.867 1.58 583/779 218/1186 190/328 190/328 24/44 69/117 59 50 13 926 2,415 5.22 0.927 2.05 229/102 41/27 63/20 20/6 7/0 6/5
15 46 10 1,925 10,961 11.39 0.941 1.75 382/350 86/71 123/48 123/48 8/6 21/51 60 44 13 1,703 6,996 8.22 0.916 1.83 381/267 199/404 165/85 75/118 17/10 34/64
16 64 9 1,552 5,071 6.53 0.926 1.94 359/220 98/60 114/35 114/35 3/8 6/3 61 59 4 2,006 10,532 10.50 0.891 1.69 327/391 175/582 102/192 44/137 13/54 30/38
17 37 7 1,895 12,248 12.93 0.945 1.66 347/472 109/465 72/129 72/129 14/49 19/29 62 73 16 1,185 4,543 7.67 0.886 1.91 278/213 139/177 143/79 74/70 13/6 6/2
18 43 6 1,783 6,340 7.11 0.943 1.90 416/322 78/86 120/69 120/69 15/14 12/14 63 131 23 2,448 6,632 5.42 0.850 1.98 538/303 234/279 193/143 98/93 18/32 31/45
19 166 33 2,866 9,723 6.79 0.795 1.89 628/393 323/278 293/116 293/116 36/33 40/44 64 197 30 3,122 11,982 7.68 0.781 1.81 589/435 361/484 257/234 114/147 33/35 48/66
20 142 34 3,440 12,799 7.44 0.783 1.88 752/432 336/385 294/196 132/149 34/35 36/52 65 30 3 332 1,685 10.15 0.988 1.69 60/85 64/263 23/54 11/61 5/27 1/4
21 71 9 1,525 12,678 16.63 0.922 1.62 263/332 121/354 84/98 30/75 16/53 29/68 66 23 4 2,523 20,630 16.35 0.954 1.86 626/325 132/64 158/34 72/27 16/5 26/34
22 70 9 2,465 6,898 5.60 0.903 2.03 633/288 191/200 231/109 99/67 19/18 15/37 67 215 41 3,254 16,033 9.85 0.762 1.78 617/461 377/533 285/298 128/172 48/68 63/66
23 24 1 402 3,010 14.98 0.983 1.60 66/97 3/15 8/10 7/8 0/0 0/5 68 86 18 1,283 7,209 11.24 0.893 1.69 223/268 171/767 99/230 47/172 19/43 24/22
24 87 6 2,347 5,280 4.50 0.905 2.09 599/298 169/184 172/133 86/78 12/5 14/15 69 192 19 3,597 40,668 22.61 0.823 1.59 585/597 301/504 269/264 103/77 26/58 78/946
25 72 14 3,512 10,063 5.73 0.856 2.06 895/319 338/203 295/93 146/59 37/25 43/54 70 37 8 n.a. n.a. n.a. n.a. n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a.
26 32 5 1,792 26,789 29.90 0.920 1.62 413/280 41/23 72/32 33/9 11/11 28/244 71 235 24 2,034 7,791 7.66 0.859 1.85 410/282 231/250 202/141 78/70 16/33 39/137
27 72 1 634 2,043 6.44 0.966 1.91 128/103 52/52 57/46 24/24 4/3 6/3 72 24 2 1,314 4,931 7.51 0.948 1.88 279/262 47/39 68/28 22/25 7/18 13/6
28 75 9 593 5,428 18.31 0.961 1.57 96/128 21/21 28/20 12/24 5/16 1/3 73 114 16 2,145 13,061 12.18 0.836 1.76 454/403 131/126 176/131 70/66 18/43 21/41
29 129 22 2,798 9,343 6.68 0.814 1.91 595/366 299/282 254/153 118/107 37/26 23/12 74 42 7 1,244 3,508 5.64 0.956 2.00 284/183 55/26 92/16 46/34 8/13 4/0
30 104 9 2,107 21,381 20.30 0.870 1.60 363/495 128/314 115/168 66/88 18/73 19/28 75 161 44 2,689 13,042 9.70 0.791 1.84 554/342 247/579 262/247 112/158 34/15 12/12
31 40 10 2,715 7,370 5.43 0.895 2.06 725/293 147/156 217/144 100/103 32/27 23/54 76 34 4 1,198 8,819 14.72 0.930 1.66 215/313 46/104 65/190 22/14 9/24 7/32
32 104 9 1,918 6,878 7.17 0.910 1.86 420/387 247/488 154/106 82/137 16/39 13/13 77 70 9 2,340 5,730 4.90 0.893 2.07 591/291 239/315 194/103 110/77 20/19 10/5
33 61 4 1,409 5,306 7.53 0.923 1.94 349/200 81/35 111/36 44/13 12/5 7/4 78 172 31 3,513 15,437 8.79 0.777 1.76 665/570 451/880 361/392 150/287 53/45 40/107
34 34 4 2,213 7,181 6.49 0.932 1.92 524/238 111/109 153/74 56/29 16/13 52/56 79 26 6 2,599 5,542 4.26 0.927 2.22 741/225 124/67 186/44 85/25 12/5 14/13
35 49 9 2,004 6,306 6.29 0.935 1.93 458/297 217/394 155/125 88/107 19/41 9/16 80 112 30 3,288 23,432 14.25 0.821 1.75 628/621 294/324 246/134 124/75 31/29 23/19
36 18 1 1,365 7,141 10.46 0.952 1.79 2889/198 79/98 68/60 30/38 13/10 15/18 81 18 1 678 2,830 8.35 0.959 1.83 146/132 11/2 34/17 6/8 1/6 0/3
37 55 6 2,450 7,970 6.51 0.941 1.94 556/318 138/269 166/84 75/72 21/38 9/4 82 125 22 1,979 9,804 9.91 0.841 1.80 416/306 189/314 152/116 60/90 19/21 14/10
38 18 2 1,904 4,469 4.69 0.955 2.13 575/229 39/26 145/24 49/10 17/9 5/11 83 54 2 915 4,027 8.80 0.948 1.79 164/115 106/291 67/36 25/51 11/28 8/12
39 54 7 1,780 5,460 6.13 0.871 1.97 443/236 144/129 159/126 68/74 7/5 28/19 84 116 12 2,531 9,667 7.64 0.866 1.86 554/413 204/232 189/174 89/85 22/17 29/24
40 60 7 1,867 5,686 6.09 0.903 1.94 415/212 241/227 174/78 96/89 32/24 13/7 85 34 5 1,749 6,155 7.04 0.939 1.92 424/237 137/138 129/54 64/65 19/21 12/15
41 73 13 2,045 4,463 4.36 0.897 2.14 558/217 166/162 179/47 86/57 21/26 5/11 86 99 20 2,979 10,234 6.87 0.812 1.91 671/439 282/432 253/149 106/129 37/58 35/23
42 74 3 1,757 8,417 9.58 0.902 1.78 346/322 150/449 134/257 59/162 16/49 26/12 87 18 5 1,871 2,559 2.74 0.968 2.60 619/147 58/35 117/29 62/13 10/3 12/6
43 127 1 n.a. n.a. n.a. n.a. n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. n.a./n.a. 88 77 16 2,926 10,935 7.47 0.860 1.89 650/326 304/413 224/153 108/109 20/17 39/53
44 24 1 428 6,269 29.29 0.978 1.43 60/128 16/44 20/18 10/17 4/1 0/1 89 20 2 1,359 6,848 10.08 0.957 1.73 270/265 71/24 72/63 38/25 7/18 17/39
45 177 40 2,436 9,984 8.20 0.808 1.81 478/392 248/590 211/198 92/183 28/29 24/15 90 54 7 612 1,398 4.57 0.957 2.07 139/87 49/42 51/32 25/9 7/4 2/0
  1. AGene Interaction Layers 43,46,52,72 failed to construct; BModules counts are listed as MCL/LCM; CNumber of enriched terms in MCL/LCM modules.