Table 1 Sizes of overlapping communities between the \(\hbox {AI-1}_{{\mathrm{MAIN}}}\) network and the ORC method results.
ID | AI-1MAIN baseline communities | All overlapping communities | The largest overlapping community | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
Community size (Number of communities) | Community size (Number of overlapped proteins) | |||||||||
Annotation | Size | ORC | ORC + SI | ORC MM | ORC MM + SI | ORC | ORC + SI | ORC MM | ORC MM + SI | |
4298 | Water transport | 11 | 11 (1) | 11 (1) | 11 (1) | 11 (1) | 11 (11) | 11 (11) | 11 (11) | 11 (11) |
1995 | Transcription/gene expression | 8 | 9 (1) | 9 (1) | 9 (1) | 9 (1) | 9 (8) | 9 (8) | 9 (8) | 9 (8) |
1534 | Oxidoreductase activity | 7 | 8 (1) | 8 (1) | 8 (1) | 8 (1) | 8 (7) | 8 (7) | 8 (7) | 8 (7) |
500 | DNA binding | 6 | 7 (1) | 7 (1) | 140 (1) | 347 (1) | 7 (6) | 7 (6) | 140 (6) | 347 (6) |
4167 | Aromatic compound metabolism | 6 | 7 (1) | 7 (1) | 7 (1) | 7 (1) | 7 (6) | 7 (6) | 7 (6) | 7 (6) |
5081 | Ribonucloprotein complex | 6 | 6 (1) | 9 (1) | 6 (1) | 58 (1) | 6 (6) | 9 (6) | 6 (6) | 58 (6) |
711 | Cytoskeleton org. and root hair elong | 9 | 15 (2) | 11 (2) | 35 (2) | 19 (1) | 9 (8) | 9 (8) | 9 (8) | 19 (9) |
5027 | TCA cycle | 8 | 11 (3) | 10 (2) | 18 (2) | 27 (2) | 5 (5) | 7 (7) | 15 (7) | 24 (7) |
1652 | Auxin signaling | 16 | 28 (4) | 75 (3) | 109 (2) | 347 (1) | 21 (13) | 70 (14) | 50 (15) | 347 (16) |
2535 | Nucleosome assembly | 13 | 24 (4) | 29 (4) | 30 (3) | 29 (4) | 8 (8) | 10 (10) | 11 (11) | 10 (10) |
5249 | Potassium transport and kinase act | 9 | 19 (4) | 17 (4) | 50 (1) | 58 (1) | 6 (6) | 6 (6) | 50 (9) | 58 (9) |
456 | DNA repair and ubiquitination | 8 | 12 (3) | 12 (4) | 140 (1) | 60 (2) | 7 (6) | 6 (5) | 140 (8) | 59 (7) |
899 | Ubiquitination | 7 | 8 (2) | 8 (2) | 159 (1) | 269 (1) | 5 (4) | 5 (4) | 159 (7) | 269 (7) |
1568 | Transcription and nitrogen meta | 7 | 36 (6) | 24 (4) | 275 (4) | 361 (2) | 3 (2) | 5 (4) | 140 (3) | 347 (6) |
4080 | Calmodulin binding | 9 | 13 (3) | 13 (3) | 13 (1) | 13 (1) | 5 (5) | 5 (5) | 13 (9) | 13 (9) |
4932 | BR signaling and phosphoprotein bind | 10 | 17 (4) | 15 (4) | 22 (2) | 347 (1) | 6 (5) | 5 (5) | 12 (9) | 347 (10) |
2796 | RNA binding | 10 | 15 (3) | 13 (3) | 121 (3) | 21 (2) | 8 (8) | 5 (5) | 8 (8) | 9 (9) |
3963 | mRNA splicing | 6 | 15 (4) | 17 (4) | 190 (2) | 269 (1) | 4 (3) | 5 (3) | 159 (5) | 269 (6) |
5255 | Seed germ. and GB and JA signaling | 7 | 29 (2) | 43 (4) | 59 (2) | 323 (3) | 8 (6) | 6 (3) | 8 (6) | 9 (3) |
4617 | Ubiquitination | 40 | 60 (10) | 59 (12) | 104 (7) | 437 (7) | 18 (17) | 16 (15) | 28 (27) | 32 (28) |
3347 | No enriched GO annotations | 14 | 36 (8) | 51 (9) | 159 (1) | 269 (1) | 10 (6) | 9 (5) | 159 (14) | 269 (14) |
4716 | Transmembrane transport | 350 | 526 (48) | 533 (52) | 790 (15) | 1310 (20) | 158 (158) | 114 (114) | 354 (315) | 332 (306) |
369 | Ubiquitin-dependent degradation | 6 | 17 (5) | 17 (5) | 299 (2) | 328 (2) | 3 (2) | 3 (2) | 140 (4) | 59 (4) |
1784 | No enriched GO annotations | 6 | 14 (3) | 20 (4) | 28 (2) | 379 (3) | 4 (4) | 3 (2) | 10 (5) | 347 (3) |
2706 | No enriched GO annotations | 22 | 58 (9) | 108 (10) | 148 (4) | 484 (4) | 9 (8) | 8 (7) | 46 (19) | 77 (19) |
1861 | Vesicle trafficking | 83 | 314 (27) | 274 (26) | 893 (13) | 1186 (11) | 16 (16) | 16 (16) | 107 (70) | 89 (70) |
