18. Data tables
18. Data tables
These tables are the -network results behind the figures — every entry computed on the Twist1 IID+TRRUST data.
18.1 Per-network results (40 scale-free networks, Fig. 1)
| Rank | Gene | NetPert weight | BC-sub rank | Out-degree | Drugs |
|---|---|---|---|---|---|
| 1 | Pdgfra | 2.13e-02 | 3 | 373 | AC-710, BMS-536924, CP-673451 |
| 2 | Htt | 1.80e-02 | 1 | 1523 | — |
| 3 | Tp53 | 1.76e-02 | 4 | 2321 | — |
| 4 | Ctnnb1 | 1.53e-02 | 6 | 1236 | CCT-031374, ICG-001, PNU-74654 |
| 5 | Cdh1 | 1.51e-02 | 5 | 933 | — |
| 6 | Zranb1 | 1.43e-02 | 2 | 3868 | — |
| 7 | Vim | 1.37e-02 | 7 | 863 | — |
| 8 | Ppia | 1.36e-02 | 27 | 883 | L-proline, TMN-355, cyclosporin-A |
| 9 | Stat3 | 1.28e-02 | 10 | 618 | APcK-110, STAT3-inhibitor-VI, WP1066 |
| 10 | Clu | 1.28e-02 | 20 | 310 | — |
| 11 | Stub1 | 1.26e-02 | 25 | 691 | — |
| 12 | Nfkb1 | 1.25e-02 | 17 | 683 | SP-100030, andrographolide, arglabin |
| 13 | Ep300 | 1.15e-02 | 14 | 1371 | C646, I-CBP-112, SGC-CBP30 |
| 14 | Sox2 | 1.14e-02 | 8 | 1386 | — |
| 15 | Col2a1 | 1.08e-02 | 9 | 70 | — |
| 16 | Rela | 1.08e-02 | 19 | 679 | BAY-11-7082, NFKB-activation-inhibitor-II, acetylcysteine |
| 17 | Kif23 | 1.07e-02 | 21 | 965 | — |
| 18 | Hif1a | 1.04e-02 | 40 | 464 | 2-methoxyestradiol, 3, 3'-diindolylmethane |
| 19 | Hdac6 | 1.02e-02 | 15 | 861 | ACY-1215, JNJ-26481585, PCI-24781 |
| 20 | H4c1 | 1.02e-02 | 12 | 1833 | — |
| 21 | Pdgfrb | 1.01e-02 | 44 | 304 | AC-710, BMS-536924, CP-673451 |
| 22 | Stau1 | 9.53e-03 | 13 | 1463 | — |
| 23 | Hdac1 | 9.46e-03 | 54 | 1116 | 4SC-202, ACY-1215, AR-42 |
| 24 | Ikbkb | 9.44e-03 | 50 | 302 | AZD3264, BMS-345541, IKK-16 |
| 25 | Tnf | 9.16e-03 | 18 | 387 | CPI-1189, JTE-607, SB-203580 |
| 26 | Eif2b5 | 8.66e-03 | 35 | 207 | — |
| 27 | Cul4a | 8.58e-03 | 26 | 790 | — |
| 28 | Hdac2 | 8.53e-03 | 67 | 878 | ACY-1215, CUDC-907, JNJ-26481585 |
| 29 | Esr1 | 8.39e-03 | 11 | 2305 | 17-hydroxyprogesterone-caproate, AZD9496, GDC-0810 |
| 30 | Ppp2ca | 8.32e-03 | 48 | 516 | vitamin-E |
Copy as CSV
Rank,Gene,NetPert weight,BC-sub rank,Out-degree,Drugs 1,Pdgfra,2.13e-02,3,373,AC-710, BMS-536924, CP-673451 2,Htt,1.80e-02,1,1523,— 3,Tp53,1.76e-02,4,2321,— 4,Ctnnb1,1.53e-02,6,1236,CCT-031374, ICG-001, PNU-74654 5,Cdh1,1.51e-02,5,933,— 6,Zranb1,1.43e-02,2,3868,— 7,Vim,1.37e-02,7,863,— 8,Ppia,1.36e-02,27,883,L-proline, TMN-355, cyclosporin-A 9,Stat3,1.28e-02,10,618,APcK-110, STAT3-inhibitor-VI, WP1066 10,Clu,1.28e-02,20,310,— 11,Stub1,1.26e-02,25,691,— 12,Nfkb1,1.25e-02,17,683,SP-100030, andrographolide, arglabin 13,Ep300,1.15e-02,14,1371,C646, I-CBP-112, SGC-CBP30 14,Sox2,1.14e-02,8,1386,— 15,Col2a1,1.08e-02,9,70,— 16,Rela,1.08e-02,19,679,BAY-11-7082, NFKB-activation-inhibitor-II, acetylcysteine 17,Kif23,1.07e-02,21,965,— 18,Hif1a,1.04e-02,40,464,2-methoxyestradiol, 3, 3'-diindolylmethane 19,Hdac6,1.02e-02,15,861,ACY-1215, JNJ-26481585, PCI-24781 20,H4c1,1.02e-02,12,1833,— 21,Pdgfrb,1.01e-02,44,304,AC-710, BMS-536924, CP-673451 22,Stau1,9.53e-03,13,1463,— 23,Hdac1,9.46e-03,54,1116,4SC-202, ACY-1215, AR-42 24,Ikbkb,9.44e-03,50,302,AZD3264, BMS-345541, IKK-16 25,Tnf,9.16e-03,18,387,CPI-1189, JTE-607, SB-203580 26,Eif2b5,8.66e-03,35,207,— 27,Cul4a,8.58e-03,26,790,— 28,Hdac2,8.53e-03,67,878,ACY-1215, CUDC-907, JNJ-26481585 29,Esr1,8.39e-03,11,2305,17-hydroxyprogesterone-caproate, AZD9496, GDC-0810 30,Ppp2ca,8.32e-03,48,516,vitamin-E
18.2 Top 30 ranked genes on the 120-node network (Figs. 4–5, section 12)
| Gene | log2FC | Drug | IC50 (nM) | Dissemination % | NetPert rank |
|---|---|---|---|---|---|
| Sema5a | 2.77 | Gö-6976 | 11.48 | 0.0 | 1133 |
| Ncam1 | 3.10 | SB-525334 | 77.51 | 13.6 | 962 |
| Emilin1 | 3.46 | Taxol | 6.012 | 15.4 | 1089 |
| Pcolce | 4.17 | Sorafenib | 151.2 | 26.7 | 1100 |
| Ptprv | 2.53 | kb-NB142-70 | 106.9 | 31.7 | 1196 |
| Olfml3 | 3.44 | Genistein | 614 | 33.3 | 1172 |
| Fut1 | 4.34 | AMD3100 | 16280 | 50.0 | 1179 |
| Tgfbi | 2.73 | Batimastat | 1765 | 50.0 | 1135 |
| Plekhg1 | 2.34 | C021.2HCl | 992.3 | 50.0 | 1102 |
| Spock2 | 3.08 | Gö-6983 | 1043 | 52.3 | 1171 |
| Cbfa2t3 | 4.27 | CP 690550 | 1397 | 59.1 | 1021 |
| Mme | 3.19 | PF-543 | 10822 | 64.7 | 149 |
| Unc5b | 3.32 | SKI-5C | 197165 | 70.0 | 1087 |
| Plxna4 | 2.83 | GNF 5837 | 31084 | 72.9 | 1043 |
| Fat4 | 4.28 | CID-755636 | 3369 | 81.2 | 1109 |
| Cacna1c | 3.06 | CID-2011756 | 9787 | 81.2 | 447 |
| Gramd1b | 2.76 | GM6001 | 36749 | 83.3 | 1123 |
| Col6a1 | 1.91 | Isradipine | 32800 | 94.7 | 1067 |
Copy as CSV
Gene,log2FC,Drug,IC50 (nM),Dissemination %,NetPert rank Sema5a,2.77,Gö-6976,11.48,0.0,1133 Ncam1,3.10,SB-525334,77.51,13.6,962 Emilin1,3.46,Taxol,6.012,15.4,1089 Pcolce,4.17,Sorafenib,151.2,26.7,1100 Ptprv,2.53,kb-NB142-70,106.9,31.7,1196 Olfml3,3.44,Genistein,614,33.3,1172 Fut1,4.34,AMD3100,16280,50.0,1179 Tgfbi,2.73,Batimastat,1765,50.0,1135 Plekhg1,2.34,C021.2HCl,992.3,50.0,1102 Spock2,3.08,Gö-6983,1043,52.3,1171 Cbfa2t3,4.27,CP 690550,1397,59.1,1021 Mme,3.19,PF-543,10822,64.7,149 Unc5b,3.32,SKI-5C,197165,70.0,1087 Plxna4,2.83,GNF 5837,31084,72.9,1043 Fat4,4.28,CID-755636,3369,81.2,1109 Cacna1c,3.06,CID-2011756,9787,81.2,447 Gramd1b,2.76,GM6001,36749,83.3,1123 Col6a1,1.91,Isradipine,32800,94.7,1067
18.3 Accuracy by network type (AUROC, Figs. 8 and 16)
| Score pair | Spearman rho | Top-20 overlap |
|---|---|---|
| NetPert – BC (driver-to-response) | 0.58 | 16/20 |
| NetPert – BC (full network) | 0.59 | 17/20 |
| NetPert – out-degree | 0.51 | 2/20 |
| NetPert – driver PPR | 0.79 | 6/20 |
| BC (driver-to-response) – BC (full) | -0.82 | 18/20 |
Copy as CSV
Score pair,Spearman rho,Top-20 overlap NetPert – BC (driver-to-response),0.58,16/20 NetPert – BC (full network),0.59,17/20 NetPert – out-degree,0.51,2/20 NetPert – driver PPR,0.79,6/20 BC (driver-to-response) – BC (full),-0.82,18/20
18.4 Accuracy by number of responses (AUROC, Fig. 9)
| Edges removed | NetPert rho | Betweenness rho | NetPert top-20 overlap |
|---|---|---|---|
| 10% | 0.948 ± 0.004 | 0.886 ± 0.009 | 17.7/20 |
| 25% | 0.889 ± 0.007 | 0.723 ± 0.003 | 11.0/20 |
| 50% | 0.775 ± 0.004 | 0.520 ± 0.020 | 9.7/20 |
18.5 Stability under rewiring (Spearman ρ, Fig. 10)
| Relaxation r | Spearman vs r = 0.5 | Top-20 overlap |
|---|---|---|
| 0.10 | 0.9976 | 18/20 |
| 0.25 | 0.9992 | 18/20 |
| 0.50 | 1.0000 | 20/20 |
| 0.75 | 0.9991 | 15/20 |
| 0.90 | 0.9966 | 11/20 |
| 0.99 | 0.9872 | 5/20 |
18.6 Accuracy by network type × number of responses (AUROC, 8 networks per cell)
| Path type | Genes | Median weight | In top-20 |
|---|---|---|---|
| DIR (driver- and response-adjacent) | 154 | 3.80e-03 | 20/20 |
| DI (driver-adjacent only) | 51 | 2.39e-04 | 0/20 |
| IR (response-adjacent only) | 838 | 1.25e-04 | 0/20 |
| I (neither) | 156 | 2.65e-06 | 0/20 |
Copy as CSV
Path type,Genes,Median weight,In top-20 DIR (driver- and response-adjacent),154,3.80e-03,20/20 DI (driver-adjacent only),51,2.39e-04,0/20 IR (response-adjacent only),838,1.25e-04,0/20 I (neither),156,2.65e-06,0/20
18.7 Parameter sweep: relaxation r × time steps n_t (20 scale-free networks)
Each cell shows mean AUROC / mean top-20 overlap with the default setting (r = 0.5, n_t = 16).
| Check | Value |
|---|---|
| Drop TRRUST directed edges (531 in subnetwork) | rank rho = 0.945; top-20 overlap 16/20 |
| DIR genes in top-10 | 10/10 |
| DIR genes in top-20 | 20/20 |
| DIR genes in top-50 | 50/50 |
| DIR genes in top-100 | 100/100 |
| DIR genes in top-200 | 149/200 |
Copy as CSV
Check,Value Drop TRRUST directed edges (531 in subnetwork),rank rho = 0.945; top-20 overlap 16/20 DIR genes in top-10,10/10 DIR genes in top-20,20/20 DIR genes in top-50,50/50 DIR genes in top-100,100/100 DIR genes in top-200,149/200