balanced_dataset_comparison

ROC curves in Figure 1 balanced dataset 9 balanced dataset 3

balanced dataset 9 (AUC = 0.808) - 0.00076

balanced dataset 3 (AUC = 0.806) 0.96913 -
balanced dataset 6 (AUC = 0.804) 0.87765 0.90839
balanced dataset 4 (AUC = 0.803) 0.85352 0.88929
balanced dataset 8 (AUC = 0.803) 0.85083 0.88471
balanced dataset 5 (AUC = 0.801) 0.78412 0.80480
balanced dataset 2 (AUC = 0.800) 0.71443 0.75762
balanced dataset 1 (AUC = 0.797) 0.63364 0.65683
balanced dataset 7 (AUC = 0.785) 0.27380 0.29162
balanced dataset 10 (AUC = 0.780) 0.16465 0.18279

Significance Level (alpha): 0.01

Upper Triangle: AUC differences
Bottom Triangle: p-values
p-value <0.01
p-value >0.01

Página 1
 balanced_dataset_comparison
balanced dataset 6 balanced dataset 4 balanced dataset 8 balanced dataset 5

0.00294 0.00347 0.00355 0.00539

0.00218 0.00271 0.00279 0.00463
- 0.00053 0.00061 0.00245
0.97803 - 0.00008 0.00192
0.97425 0.99687 - 0.00184
0.90036 0.92194 0.92251 -
0.84503 0.86164 0.87071 0.94612
0.74310 0.76037 0.76904 0.84123
0.32896 0.36641 0.37185 0.41052
0.23822 0.24565 0.23161 0.27730

Página 2
 balanced_dataset_comparison
balanced dataset 2 balanced dataset 1 balanced dataset 7 balanced dataset 10

0.00674 0.00934 0.02152 0.02673

0.00598 0.00858 0.02076 0.02597
0.00380 0.00640 0.01858 0.02379
0.00327 0.00587 0.01805 0.02326
0.00319 0.00579 0.01797 0.02318
0.00135 0.00395 0.01613 0.02134
- 0.00260 0.01478 0.01999
0.89703 - 0.01218 0.01739
0.45365 0.53776 - 0.00521
0.32835 0.37874 0.79070 -

Página 3
 network_vs_netfeatures
ROC curves in Figure 2
net only_ppi_metabolic_features
net (AUC = 0.773 ) - 0.00781
only_ppi_metabolic_features (AUC = 0.765) 0.30160 -
only_ppi_other_features (AUC = 0.763) 0.07085 0.80155
only_ppi_reg_features (AUC = 0.757 ) 0.00346 0.32181
only ppi inbetppi (AUC = 0.748) 0.00376 0.00137
ppi (AUC = 0.747) 0.00157 0.01141
inbetppi (AUC = 0.701) 0.00000 0.00000
inbet (AUC = 0.628) 0.00000 0.00000
c (AUC = 0.615) 0.00000 0.00000
cent (AUC = 0.559) 0.00000 0.00000
regin (AUC = 0.547) 0.00000 0.00000
metin (AUC = 0.518) 0.00000 0.00000
regout (AUC = 0.514) 0.00000 0.00000
metout (AUC = 0.513) 0.00000 0.00000
inbetmet (AUC = 0.512) 0.00000 0.00000
ident (AUC = 0.508) 0.00000 0.00000
inbetreg (AUC = 0.502 0.00000 0.00000

Significance Level (alpha): 0.01

Upper Triangle: AUC differences
Bottom Triangle: p-values
p-value <0.01
p-value >0.01

Página 4
 network_vs_netfeatures

only_ppi_other_features only_ppi_reg_features only ppi inbetppi ppi inbetppi

0.00983 0.01614 0.02488 0.02629 0.07230
0.0020 0.00833 0.0171 0.0185 0.0645
- 0.00631 0.01505 0.01646 0.06247
0.40235 - 0.00874 0.01015 0.05616
0.06489 0.28339 - 0.00141 0.04742
0.02782 0.20647 0.82968 - 0.04601
0.00000 0.00000 0.00020 0.00015 -
0.00000 0.00000 0.00000 0.00000 0.00003
0.00000 0.00000 0.00000 0.00000 0.00004
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 0.00000 0.00000 0.00000

Página 5
 network_vs_netfeatures

inbet c cent regin metin regout metout

0.14443 0.15794 0.21418 0.22590 0.25469 0.25878 0.28550
0.1366 0.1501 0.2064 0.2181 0.2469 0.2510 0.2523
0.13460 0.14811 0.20435 0.21607 0.24486 0.24895 0.25028
0.12829 0.14180 0.19804 0.20975 0.23855 0.24263 0.24396
0.11955 0.13306 0.18930 0.20101 0.22981 0.23389 0.23522
0.11814 0.13165 0.18789 0.19961 0.22840 0.23249 0.25921
0.07213 0.08564 0.14188 0.15360 0.18239 0.18648 0.18780
- 0.01351 0.06975 0.08147 0.11026 0.11435 0.11567
0.52636 - 0.05624 0.06796 0.09675 0.10084 0.10217
0.00027 0.01038 - 0.01172 0.04051 0.04460 0.04592
0.00503 0.01098 0.69013 - 0.02880 0.03288 0.03421
0.00000 0.00000 0.04627 0.15687 - 0.00408 0.03081
0.00000 0.00000 0.01708 0.07045 0.71755 - 0.00133
0.00000 0.00000 0.02295 0.10265 0.02863 0.90465 -
0.00000 0.00000 0.02042 0.08684 0.61284 0.83165 0.94367
0.00000 0.00000 0.00435 0.03898 0.35995 0.38143 0.66785
0.00000 0.00001 0.03353 0.01581 0.41519 0.47640 0.59240

Página 6
 network_vs_netfeatures

inbetmet ident inbetreg

0.26111 0.26472 0.27098
0.2533 0.2569 0.2632
0.25128 0.25489 0.26115
0.24497 0.24858 0.25484
0.23623 0.23984 0.24610
0.23482 0.23843 0.24469
0.18881 0.19242 0.19868
0.11668 0.12029 0.12655
0.10317 0.10678 0.11305
0.04693 0.05054 0.05680
0.03521 0.03883 0.04509
0.00642 0.01003 0.01629
0.00233 0.00595 0.01221
0.00101 0.00462 0.01088
- 0.00361 0.00987
0.73395 - 0.00626
0.62994 0.73284 -

Página 7
 network_exclusion
ROC curves in Additional File 3
net_no_ident net net_no_metin
net no ident (AUC = 0.775 ) - 0.00176 0.00228
net (AUC = 0.773) 0.27403 - 0.00053
net_no_metin (AUC = 0.772) 0.19302 0.75465 -
net_no_regin_regout_inbetreg (AUC = 0.772) 0.50843 0.81433 0.91755
net_no_inbetreg (AUC = 0.772) 0.24536 0.65887 0.84367
net_no_regout (AUC = 0.772) 0.08789 0.48281 0.72322
net_no_regin (AUC = 0.772) 0.34949 0.68811 0.82562
net_no_metout (AUC = 0.772) 0.13800 0.48097 0.69450
net_no_c (AUC = 0.771) 0.27190 0.58806 0.71163
net_no_inbetmet (AUC = 0.771) 0.08591 0.33906 0.56879
net_no_cent (AUC = 0.770) 0.11069 0.28692 0.43054
net_no_inbetppi (AUC = 0.770) 0.06880 0.24354 0.36904
net_no_c_cent_ident (AUC = 0.766) 0.05651 0.12644 0.17081
net_no_metin_metout_inbetmet (AUC = 0.764) 0.00029 0.00218 0.00260
net_no_ppi (AUC = 0.758) 0.00473 0.01150 0.01668
net_no_ppi inbetppi (AUC = 0.749) 0.00046 0.00116 0.00165

Significance Level (alpha): 0.01

Upper Triangle: AUC differences
Bottom Triangle: p-values
p-value <0.01
p-value >0.01

Página 8
 network_exclusion

net_no_regin_regout_inbetreg net_no_inbetreg net_no_regout net_no_regin

0.00273 0.00280 0.00287 0.00300
0.00097 0.00104 0.00112 0.00124
0.00044 0.00052 0.00059 0.00072
- 0.00007 0.00014 0.00027
0.98365 - 0.00007 0.00020
0.97217 0.97658 - 0.00013
0.93248 0.95338 0.96753 -
0.93958 0.92335 0.92276 0.98551
0.90193 0.87973 0.87154 0.93423
0.85209 0.78709 0.74217 0.86599
0.70638 0.60365 0.54767 0.68468
0.67492 0.55085 0.46903 0.64079
0.33773 0.26139 0.20858 0.29868
0.12210 0.02849 0.00824 0.06192
0.06311 0.02671 0.02318 0.04301
0.01106 0.00322 0.00243 0.00538

Página 9
 network_exclusion

Página 10
 network_exclusion

net_no_metout net_no_c net_no_inbetmet net_no_cent net_no_inbetppi

0.00306 0.00334 0.00355 0.00451 0.00475
0.00130 0.00159 0.00180 0.00275 0.00299
0.00078 0.00106 0.00127 0.00223 0.00247
0.00033 0.00061 0.00082 0.00178 0.00202
0.00026 0.00054 0.00075 0.00171 0.00195
0.00019 0.00047 0.00068 0.00164 0.00188
0.00006 0.00034 0.00055 0.00151 0.00175
- 0.00028 0.00049 0.00145 0.00169
0.92820 - 0.00021 0.00117 0.00141
0.81869 0.94909 - 0.00096 0.00120
0.62194 0.76029 0.74648 - 0.00024
0.55560 0.71014 0.67729 0.94351 -
0.24744 0.22729 0.29888 0.36317 0.49165
0.00532 0.05966 0.00737 0.11369 0.11329
0.02670 0.05207 0.02487 0.05672 0.06385
0.00332 0.00585 0.00279 0.00616 0.00330

Página 11
 network_exclusion

net_no_c_cent_ident net_no_metin_metout_inbetmet net_no_ppi

0.00830 0.01044 0.01656
0.00655 0.00868 0.01480
0.00602 0.00815 0.01427
0.00557 0.00771 0.01383
0.00550 0.00764 0.01376
0.00543 0.00756 0.01368
0.00530 0.00744 0.01356
0.00524 0.00737 0.01349
0.00496 0.00709 0.01321
0.00475 0.00688 0.01300
0.00379 0.00593 0.01205
0.00355 0.00569 0.01181
- 0.00213 0.00825
0.67028 - 0.00612
0.28645 0.33160 -
0.06074 0.05612 0.09722

Página 12
 network_exclusion

net_no_ppi inbetppi
0.02550
0.02374
0.02321
0.02277
0.02270
0.02262
0.02249
0.02243
0.02215
0.02194
0.02099
0.02075
0.01719
0.01506
0.00894
-

Página 13
 compartments
ROC curves in Figure 3 all compartments nucleus cytoplasm

all compartments (AUC = 0.703) - 0.04778 0.15504

nucleus (AUC = 0.655) 0.00000 - 0.10725
cytoplasm (AUC = 0.548) 0.00000 0.00000 -
mitochondrion (AUC = 0.535) 0.00000 0.00000 0.41299
other compartment (AUC = 0.524) 0.00000 0.00000 0.22180
endoplasmic reticulum (AUC = 0.506) 0.00000 0.00000 0.02688

Significance Level (alpha): 0.01

Upper Triangle: AUC differences
Bottom Triangle: p-values
p-value <0.01
p-value >0.01

Página 14
 compartments
mitochondrion other compartment endoplasmic reticulum

0.16761 0.17880 0.19709

0.11983 0.13101 0.14930
0.01257 0.02376 0.04205
- 0.01119 0.02947
0.46945 - 0.01829
0.03862 0.09545 -

Página 15
 processes
ROC curves in Figure 4
all processes Metabolic process other process
all processes (AUC = 0.667) - 0.03970 0.13101
metabolic process (AUC = 0.627) 0.00087 - 0.09131
other process (AUC = 0.536) 0.00000 0.00000 -
cell cycle (AUC = 0.534) 0.00000 0.00000 0.85991
transcription (AUC = 0.534) 0.00000 0.00000 0.84998
transport (AUC = 0.513) 0.00000 0.00000 0.08595
signal transduction (AUC = 0.502) 0.00000 0.00000 0.00100

Significance Level (alpha): 0.01

Upper Triangle: AUC differences
Bottom Triangle: p-values
p-value <0.01
p-value >0.01

Página 16
 processes

cell cycle transcription transport signal transduction

0.13314 0.13339 0.15458 0.16472
0.09344 0.09369 0.11488 0.12502
0.00213 0.00238 0.02357 0.03371
- 0.00025 0.02144 0.03158
0.98478 - 0.02119 0.03133
0.18616 0.21228 - 0.01014
0.00505 0.00642 0.44684 -

Página 17
 compartments_vs_processes
ROC curves in Figure 5
all processes and compartments
all processes and compartments (AUC = 0.753) -
all compartments (AUC = 0.703) 0.00000
all processes (AUC = 0.667) 0.00000

Significance Level (alpha): 0.01

Upper Triangle: AUC differences
Bottom Triangle: p-values
p-value <0.01
p-value >0.01

Página 18
 compartments_vs_processes

all compartments all processes

0.05000 0.08584
- 0.03584
0.04227 -

Página 19
 integrated_predictors
ROC curves in Figure 6
all data network
all data (AUC = 0.808) - 0.03484
network (AUC = 0.773) 0.00009 -
all processes and compartments (AUC = 0.753) 0.00001 0.26875

Significance Level (alpha): 0.01

Upper Triangle: AUC differences
Bottom Triangle: p-values
p-value <0.01
p-value >0.01

Página 20
 integrated_predictors

all processes and compartments

0.05441
0.01956
-

Página 21