Spreadsheet: 2352bb50-36fc-4df3-ba15-bd7a4340c63a
Sheet: Sheet1

Table S1. AUCs and p-values fo evaluations performed using either co-expression only or co-expression combined with PPI information. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8
 |  |  | AUC |  |  | p-value
Organism Pari | PPI included? | Standard | Sequence | NetCompare | Combined rank | Sequence | NetCompare | Combined rank
CEL_DME | +ppi | cell_cycle | 0.596538 | 0.731923 | 0.734231 | 0.0423487 | 0.000240638 | 0.000213942
CEL_DME | +ppi | go_BP | 0.595336 | 0.582349 | 0.621611 | 1.36737e-05 | 0.000123029 | 6.63224e-08
CEL_DME | +ppi | neuronal | 0.550809 | 0.581539 | 0.592533 | 0.0120113 | 0.000377885 | 7.95058e-05
CEL_MMU | +ppi | cell_cycle | 0.5699489999999999 | 0.623728 | 0.621911 | 0.0553168 | 0.00762428 | 0.008255760000000001
CEL_MMU | +ppi | go_BP | 0.541674 | 0.565168 | 0.5716479999999999 | 0.00178367 | 6.46246e-06 | 9.33814e-07
CEL_MMU | +ppi | neuronal | 0.555532 | 0.582141 | 0.597073 | 0.00307613 | 5.3315e-05 | 3.02318e-06
CEL_SCE | +ppi | cell_cycle | 0.695106 | 0.7013889999999999 | 0.768849 | 0.0007771060000000001 | 0.000568253 | 1.15342e-05
CEL_SCE | +ppi | go_BP | 0.615132 | 0.581459 | 0.6415069999999999 | 0.0019152 | 0.0147984 | 0.000261758
DME_MMU | +ppi | cell_cycle | 0.6733800000000001 | 0.6442129999999999 | 0.679167 | 0.00148804 | 0.00553843 | 0.00112005
DME_MMU | +ppi | go_BP | 0.571758 | 0.538682 | 0.574488 | 1.87238e-08 | 0.0009340490000000001 | 5.88835e-09
DME_MMU | +ppi | neuronal | 0.542076 | 0.575908 | 0.590776 | 0.04632559999999999 | 0.00421588 | 0.00106668
DME_SCE | +ppi | cell_cycle | 0.732456 | 0.565789 | 0.6771929999999999 | 0.00163777 | 0.110402 | 0.00955526
DME_SCE | +ppi | go_BP | 0.630208 | 0.630361 | 0.675424 | 4.15478e-05 | 4.08172e-05 | 9.78276e-08
MMU_SCE | +ppi | cell_cycle | 0.671715 | 0.515645 | 0.6200249999999999 | 0.000276079 | 0.191159 | 0.00563502
MMU_SCE | +ppi | go_BP | 0.576421 | 0.5572889999999999 | 0.5770219999999999 | 0.00145549 | 0.00967792 | 0.00136177
MMU_SCE | +ppi | [NAME] | 0.5442319999999999 | 0.567067 | 0.571853 | 0.0567262 | 0.0167299 | 0.0124126
CEL_DME | +ppi | cell_cycle | 0.596538 | 0.7103849999999999 | 0.716923 | 0.0423487 | 0.0006868670000000001 | 0.00050422
CEL_DME | +ppi | go_BP | 0.594421 | 0.5776600000000001 | 0.617837 | 1.52284e-05 | 0.000243817 | 1.40725e-07
CEL_DME | +ppi | neuronal | 0.551195 | 0.5698529999999999 | 0.587266 | 0.0115448 | 0.00163004 | 0.000169372
CEL_MMU | +ppi | cell_cycle | 0.5699489999999999 | 0.627362 | 0.6197309999999999 | 0.0553168 | 0.00648492 | 0.00907214
CEL_MMU | +ppi | go_BP | 0.541674 | 0.5664319999999999 | 0.572268 | 0.00178367 | 4.4894e-06 | 7.69229e-07
CEL_MMU | +ppi | neuronal | 0.555532 | 0.582141 | 0.597073 | 0.00307613 | 5.3315e-05 | 3.02318e-06
CEL_SCE | +ppi | cell_cycle | 0.695106 | 0.698413 | 0.767857 | 0.0007771060000000001 | 0.0006597650000000001 | 1.23025e-05
CEL_SCE | +ppi | go_BP | 0.615132 | 0.608792 | 0.658134 | 0.0019152 | 0.00293531 | 6.2397e-05
DME_MMU | +ppi | cell_cycle | 0.6733800000000001 | 0.6432869999999999 | 0.682639 | 0.00148804 | 0.005756030000000001 | 0.000941001
DME_MMU | +ppi | go_BP | 0.572271 | 0.516071 | 0.561207 | 1.42808e-08 | 0.0568638 | 1.07335e-06
DME_MMU | +ppi | neuronal | 0.542076 | 0.585577 | 0.598896 | 0.04632559999999999 | 0.0017647 | 0.000462435
DME_SCE | +ppi | cell_cycle | 0.732456 | 0.664912 | 0.7166669999999999 | 0.00163777 | 0.0134377 | 0.00281788
DME_SCE | +ppi | go_BP | 0.6337079999999999 | 0.649175 | 0.691179 | 2.52809e-05 | 3.60073e-06 | 6.7834e-09
MMU_SCE | +ppi | cell_cycle | 0.671715 | 0.499625 | 0.605632 | 0.000276079 | 0.250948 | 0.011164
MMU_SCE | +ppi | go_BP | 0.573211 | 0.5537449999999999 | 0.572975 | 0.00200159 | 0.0128919 | 0.00205296
MMU_SCE | +ppi | [NAME] | 0.5442319999999999 | 0.582113 | 0.581894 | 0.0567262 | 0.00621993 | 0.00631696
CEL_DME | +ppi | cell_death | 0.5 | 0.4375 | 0.25 | 0.25 | 0.299353 | 0.420672
CEL_DME | +ppi | cell_fate_commitment | 0.518699 | 0.614634 | 0.587263 | 0.190544 | 0.016699 | 0.0406486
CEL_DME | +ppi | cell_migration | 0.425862 | 0.44569 | 0.418103 | 0.404582 | 0.369596 | 0.416536
CEL_DME | +ppi | cell_morphogenesis | 0.588426 | 0.588889 | 0.627315 | 0.0360304 | 0.0355084 | 0.00886693
CEL_DME | +ppi | cell_surface_receptor_linked_signal_transduction | 0.599405 | 0.552976 | 0.616667 | 0.0493989 | 0.123076 | 0.0326225
CEL_DME | +ppi | cytoskeleton_organization_and_biogenesis | 0.593823 | 0.667055 | 0.676573 | 0.0273117 | 0.0010872 | 0.0006442150000000001
CEL_DME | +ppi | gastrulation | 0.228571 | 0.485714 | 0.242857 | 0.465254 | 0.25 | 0.459426
CEL_DME | +ppi | morphogenesis_of_an_epithelium | 0.583128 | 0.535391 | 0.5925929999999999 | 0.0594373 | 0.153217 | 0.0471781
CEL_DME | +ppi | vesicle-mediated_transport | 0.739583 | 0.4062500000000001 | 0.619792 | 0.0189956 | 0.378137 | 0.0937368
CEL_MMU | +ppi | cell_death | 0.666667 | 0.666667 | 0.75 | 0.119875 | 0.119875 | 0.0722111
CEL_MMU | +ppi | cell_fate_commitment | 0.500455 | 0.442998 | 0.469547 | 0.247955 | 0.45013 | 0.376736
CEL_MMU | +ppi | cell_migration | 0.51853 | 0.5544 | 0.5609729999999999 | 0.165637 | 0.0500348 | 0.03775299999999999
CEL_MMU | +ppi | cell_morphogenesis | 0.559145 | 0.5851569999999999 | 0.603448 | 0.0511524 | 0.0169467 | 0.00662647
CEL_MMU | +ppi | cell_surface_receptor_linked_signal_transduction | 0.537656 | 0.556082 | 0.570529 | 0.0881858 | 0.0415907 | 0.0204426
CEL_MMU | +ppi | cytoskeleton_organization_and_biogenesis | 0.540021 | 0.627859 | 0.6169439999999999 | 0.147726 | 0.021481 | 0.029063
CEL_MMU | +ppi | gastrulation | 0.6857139999999999 | 0.904762 | 0.8523809999999999 | 0.0395839 | 0.000605367 | 0.002042
CEL_MMU | +ppi | morphogenesis_of_an_epithelium | 0.5445 | 0.6970000000000001 | 0.6495000000000001 | 0.13712 | 0.0019748 | 0.0109537
CEL_MMU | +ppi | regulation_of_signal_transduction | 0.5 | 0.25 | 0.3125 | 0.25 | 0.420672 | 0.386686
CEL_MMU | +ppi | vesicle-mediated_transport | 0.581448 | 0.432127 | 0.5181 | 0.109603 | 0.364093 | 0.212624
CEL_RNA | +ppi | polymerase_II_promoter | 0.532086 | 0.6470589999999999 | 0.6122989999999999 | 0.189887 | 0.0468367 | 0.0778373
CEL_SCE | +ppi | cell_morphogenesis | 0.395299 | 0.7371789999999999 | 0.6047009999999999 | 0.411219 | 0.00904915 | 0.0887814
CEL_SCE | +ppi | cell_surface_receptor_linked_signal_transduction | 0.618182 | 0.209091 | 0.409091 | 0.106258 | 0.480667 | 0.347981
CEL_SCE | +ppi | cytoskeleton_organization_and_biogenesis | 0.769324 | 0.727053 | 0.851449 | 0.000849743 | 0.00338337 | 3.30485e-05
CEL_SCE | +ppi | vesicle-mediated_transport | 0.82 | 0.82 | 1 | 0.0174886 | 0.0174886 | 0.0013945
DME_MMU | +ppi | cell_death | 0.574851 | 0.5572039999999999 | 0.581159 | 0.0275777 | 0.0555441 | 0.0208528
DME_MMU | +ppi | cell_fate_commitment | 0.477885 | 0.5112829999999999 | 0.482108 | 0.37954 | 0.179926 | 0.357667
DME_MMU | +ppi | cell_migration | 0.610022 | 0.5492859999999999 | 0.602861 | 0.000194505 | 0.0330358 | 0.000419792
DME_MMU | +ppi | cell_morphogenesis | 0.616896 | 0.529413 | 0.6060519999999999 | 1.89636e-05 | 0.0798501 | 8.26543e-05
DME_MMU | +ppi | cell_surface_receptor_linked_signal_transduction | 0.615551 | 0.5396569999999999 | 0.6028089999999999 | 4.60301e-05 | 0.0497994 | 0.000219076
DME_MMU | +ppi | cytoskeleton_organization_and_biogenesis | 0.485714 | 0.6622709999999999 | 0.570696 | 0.290745 | 0.0040592 | 0.0734066
DME_MMU | +ppi | gastrulation | 0.487631 | 0.583179 | 0.538343 | 0.291988 | 0.0384514 | 0.127725
DME_MMU | +ppi | morphogenesis_of_an_epithelium | 0.731915 | 0.5872339999999999 | 0.7195739999999999 | 0.000310296 | 0.0557719 | 0.000557559
DME_MMU | +ppi | regulation_of_signal_transduction | 0.575758 | 0.454545 | 0.5057929999999999 | 0.07671019999999999 | 0.365051 | 0.234429
DME_MMU | +ppi | vesicle-mediated_transport | 0.673141 | 0.536903 | 0.660377 | 0.00166104 | 0.140731 | 0.00298351
DME_RNA | +ppi | polymerase_II_promoter | 0.509058 | 0.7583329999999999 | 0.669203 | 0.223581 | 3.78926e-05 | 0.0032719
DME_SCE | +ppi | cell_morphogenesis | 0.65102 | 0.706803 | 0.7687069999999999 | 0.014786 | 0.00246257 | 0.000201212
DME_SCE | +ppi | cell_surface_receptor_linked_signal_transduction | 0.840278 | 0.625 | 0.8263889999999999 | 0.00138396 | 0.0770449 | 0.00194859
DME_SCE | +ppi | cytoskeleton_organization_and_biogenesis | 0.583333 | 0.668333 | 0.646667 | 0.101164 | 0.0230776 | 0.0356167
DME_SCE | +ppi | vesicle-mediated_transport | 0.683824 | 0.530637 | 0.609069 | 0.0117942 | 0.185202 | 0.05973949999999999
MMU_RNA | +ppi | polymerase_II_promoter | 0.60418 | 0.6014729999999999 | 0.673056 | 0.00933344 | 0.010639 | 0.000136461
MMU_SCE | +ppi | cell_morphogenesis | 0.459524 | 0.5104759999999999 | 0.481905 | 0.351915 | 0.222444 | 0.297297
MMU_SCE | +ppi | cell_surface_receptor_linked_signal_transduction | 0.6969700000000001 | 0.30303 | 0.464646 | 0.0320918 | 0.462853 | 0.295105
MMU_SCE | +ppi | cytoskeleton_organization_and_biogenesis | 0.432692 | 0.625 | 0.5 | 0.347107 | 0.086405 | 0.25
MMU_SCE | +ppi | vesicle-mediated_transport | 0.885417 | 0.734776 | 0.8693909999999999 | 7.52549e-07 | 0.001111 | 1.9019e-06
RNA_SCE | +ppi | polymerase_II_promoter | 0.509058 | 0.7583329999999999 | 0.669203 | 0.223581 | 3.78926e-05 | 0.0032719
CEL_DME | -ppi | cell_death | 0.5 | 0.4375 | 0.25 | 0.25 | 0.299353 | 0.420672
CEL_DME | -ppi | cell_fate_commitment | 0.518699 | 0.6319779999999999 | 0.595393 | 0.190544 | 0.00872042 | 0.0317466
CEL_DME | -ppi | cell_migration | 0.425862 | 0.472414 | 0.437931 | 0.404582 | 0.313802 | 0.38402
CEL_DME | -ppi | cell_morphogenesis | 0.588426 | 0.565278 | 0.6023149999999999 | 0.0360304 | 0.0702301 | 0.0227555
CEL_DME | -ppi | cell_surface_receptor_linked_signal_transduction | 0.599405 | 0.595833 | 0.641667 | 0.0493989 | 0.053546 | 0.0165817
CEL_DME | -ppi | cytoskeleton_organization_and_biogenesis | 0.593823 | 0.6414139999999999 | 0.660839 | 0.0273117 | 0.00394476 | 0.00151011
CEL_DME | -ppi | gastrulation | 0.228571 | 0.242857 | 0.157143 | 0.465254 | 0.459426 | 0.48533
CEL_DME | -ppi | morphogenesis_of_an_epithelium | 0.600155 | 0.6253879999999999 | 0.664984 | 0.0376243 | 0.0179648 | 0.00446592
CEL_DME | -ppi | vesicle-mediated_transport | 0.739583 | 0.4375 | 0.651042 | 0.0189956 | 0.339143 | 0.0658171
CEL_MMU | -ppi | cell_death | 0.666667 | 0.666667 | 0.75 | 0.119875 | 0.119875 | 0.0722111
CEL_MMU | -ppi | cell_fate_commitment | 0.500455 | 0.442998 | 0.469547 | 0.247955 | 0.45013 | 0.376736
CEL_MMU | -ppi | cell_migration | 0.51853 | 0.555124 | 0.559731 | 0.165637 | 0.0485529 | 0.0398784
CEL_MMU | -ppi | cell_morphogenesis | 0.559145 | 0.5849329999999999 | 0.601949 | 0.0511524 | 0.0171289 | 0.00719361
CEL_MMU | -ppi | cell_surface_receptor_linked_signal_transduction | 0.537656 | 0.556082 | 0.570813 | 0.0881858 | 0.0415907 | 0.020137
CEL_MMU | -ppi | cytoskeleton_organization_and_biogenesis | 0.540021 | 0.611746 | 0.610707 | 0.147726 | 0.0333458 | 0.0342582
CEL_MMU | -ppi | gastrulation | 0.6857139999999999 | 0.904762 | 0.8523809999999999 | 0.0395839 | 0.000605367 | 0.002042
CEL_MMU | -ppi | morphogenesis_of_an_epithelium | 0.5445 | 0.6970000000000001 | 0.652 | 0.13712 | 0.0019748 | 0.0101016
CEL_MMU | -ppi | regulation_of_signal_transduction | 0.5 | 0.25 | 0.3125 | 0.25 | 0.420672 | 0.386686
CEL_MMU | -ppi | vesicle-mediated_transport | 0.581448 | 0.457014 | 0.533937 | 0.109603 | 0.323451 | 0.184391
CEL_RNA | -ppi | polymerase_II_promoter | 0.532086 | 0.6764709999999999 | 0.657754 | 0.189887 | 0.0286728 | 0.0394401
CEL_SCE | -ppi | cell_morphogenesis | 0.395299 | 0.773504 | 0.662393 | 0.411219 | 0.00392814 | 0.0378775
CEL_SCE | -ppi | cell_surface_receptor_linked_signal_transduction | 0.618182 | 0.209091 | 0.409091 | 0.106258 | 0.480667 | 0.347981
CEL_SCE | -ppi | cytoskeleton_organization_and_biogenesis | 0.769324 | 0.816425 | 0.879227 | 0.000849743 | 0.00014467 | 9.29077e-06
CEL_SCE | -ppi | vesicle-mediated_transport | 0.82 | 0.82 | 1 | 0.0174886 | 0.0174886 | 0.0013945
DME_MMU | -ppi | cell_death | 0.574851 | 0.543052 | 0.575959 | 0.0275777 | 0.0894972 | 0.0262858
DME_MMU | -ppi | cell_fate_commitment | 0.477885 | 0.466038 | 0.447534 | 0.37954 | 0.42998 | 0.476204
DME_MMU | -ppi | cell_migration | 0.606637 | 0.5288309999999999 | 0.591047 | 0.00030942 | 0.0956269 | 0.00145462
DME_MMU | -ppi | cell_morphogenesis | 0.614383 | 0.519013 | 0.600192 | 3.008e-05 | 0.13067 | 0.000189028
DME_MMU | -ppi | cell_surface_receptor_linked_signal_transduction | 0.615551 | 0.490852 | 0.5744659999999999 | 4.60301e-05 | 0.308099 | 0.00398466
DME_MMU | -ppi | cytoskeleton_organization_and_biogenesis | 0.485714 | 0.6424909999999999 | 0.559341 | 0.290745 | 0.00868822 | 0.0943923
DME_MMU | -ppi | gastrulation | 0.487631 | 0.5875079999999999 | 0.5391159999999999 | 0.291988 | 0.0333748 | 0.125604
DME_MMU | -ppi | morphogenesis_of_an_epithelium | 0.731915 | 0.354043 | 0.559574 | 0.000310296 | 0.489224 | 0.101081
DME_MMU | -ppi | regulation_of_signal_transduction | 0.575758 | 0.472371 | 0.519608 | 0.07671019999999999 | 0.322654 | 0.197852
DME_MMU | -ppi | vesicle-mediated_transport | 0.673141 | 0.531909 | 0.6573249999999999 | 0.00166104 | 0.154232 | 0.00341346
DME_RNA | -ppi | polymerase_II_promoter | 0.509058 | 0.840217 | 0.7231879999999999 | 0.223581 | 1.51481e-07 | 0.000265957
DME_SCE | -ppi | cell_morphogenesis | 0.65102 | 0.694558 | 0.7544219999999999 | 0.014786 | 0.00378808 | 0.000376647
DME_SCE | -ppi | cell_surface_receptor_linked_signal_transduction | 0.8588239999999999 | 0.641176 | 0.8294119999999999 | 0.0005435090000000001 | 0.05695000000000001 | 0.00122283
DME_SCE | -ppi | cytoskeleton_organization_and_biogenesis | 0.583333 | 0.616667 | 0.615 | 0.101164 | 0.0608363 | 0.062536
DME_SCE | -ppi | vesicle-mediated_transport | 0.683824 | 0.530637 | 0.6139709999999999 | 0.0117942 | 0.185202 | 0.0546256
MMU_RNA | -ppi | polymerase_II_promoter | 0.5440229999999999 | 0.6243679999999999 | 0.609425 | 0.0962275 | 0.00352547 | 0.00769829
MMU_SCE | -ppi | cell_morphogenesis | 0.459524 | 0.4761900000000001 | 0.451905 | 0.351915 | 0.311804 | 0.368845
MMU_SCE | -ppi | cell_surface_receptor_linked_signal_transduction | 0.6969700000000001 | 0.434343 | 0.565657 | 0.0320918 | 0.337933 | 0.148647
MMU_SCE | -ppi | cytoskeleton_organization_and_biogenesis | 0.432692 | 0.625 | 0.5 | 0.347107 | 0.086405 | 0.25
MMU_SCE | -ppi | vesicle-mediated_transport | 0.885417 | 0.722756 | 0.866987 | 7.52549e-07 | 0.00173789 | 2.17886e-06
RNA_SCE | -ppi | polymerase_II_promoter | 0.509058 | 0.840217 | 0.7231879999999999 | 0.223581 | 1.51481e-07 | 0.000265957