Table S7. Co-regulated pairs of paralogous proteins
Complex ID Complex nameAssociated transcipt name paralog 1Description paralog 1Associated transcipt name paralog 2Description paralog 2Significant data point paralog 1Fold change paralog 1 (log2)Significant data point paralog 2Fold change paralog 2 (log2)Paralog co-regulationTranscriptional regulationProtein ID paralog 1Protein ID paralog 2Gene ID paralog 1 (human ortholog)Gene ID paralog 2 (human ortholog)
embl_complex_004; embl_complex_075; embl_complex_089; embl_complex_208 BAF complex; RSC; Sin3-CI; RNA polymerase II complex, chromatin structure modifying SMARCD3 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 [Source:HGNC Symbol;Acc:11108] SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 [Source:HGNC Symbol;Acc:11106] D3/D0 2.486455556 D3/D0 1.142347917 opposite sign both paralogs ENSMUSP00000030791 ENSMUSP00000023759 ENSG00000082014 ENSG00000066117
embl_complex_004; embl_complex_075; embl_complex_089; embl_complex_208; embl_complex_088; embl_complex_113; embl_complex_118 BAF complex; RSC; Sin3-CI; RNA polymerase II complex, chromatin structure modifying; emerin C32; GST-Smad; N-CoR-1 SMARCC2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 [Source:HGNC Symbol;Acc:11105] SMARCC1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 [Source:HGNC Symbol;Acc:11104] D3/D0 -1.534283333 D3/D0 0.85406691 opposite sign NA ENSMUSP00000100868 ENSMUSP00000086094 ENSG00000139613 ENSG00000173473
embl_complex_131 cAMP-dependent protein kinase PRKAR1A protein kinase, cAMP-dependent, regulatory, type I, alpha [Source:HGNC Symbol;Acc:9388] PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta [Source:HGNC Symbol;Acc:9392] iPS/D12 -1.9483125 iPS/D12 1.58403125 opposite sign NA ENSMUSP00000102288 ENSMUSP00000003079 ENSG00000108946 ENSG00000005249
embl_complex_103 COPI ARFGAP2 ADP-ribosylation factor GTPase activating protein 2 [Source:HGNC Symbol;Acc:13504] ARFGAP3 ADP-ribosylation factor GTPase activating protein 3 [Source:HGNC Symbol;Acc:661] D3/D0 1.60578125 D3/D0 -2.140328125 opposite sign one paralog ENSMUSP00000078920 ENSMUSP00000064893 ENSG00000149182 ENSG00000242247
embl_complex_070 COPII SEC23B Sec23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:10702] SEC23A Sec23 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10701] D3/D0 1.166985294 D3/D0 -1.281941176 opposite sign one paralog ENSMUSP00000122819 ENSMUSP00000021375 ENSG00000101310 ENSG00000100934
embl_complex_070 COPII SEC31A SEC31 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:17052] SEC31B SEC31 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:23197] D3/D0 -0.865955882 D3/D0 2.593352941 opposite sign NA ENSMUSP00000092157 ENSMUSP00000064900 ENSG00000138674 ENSG00000075826
embl_complex_122 eIF4F EIF4A3 eukaryotic translation initiation factor 4A3 [Source:HGNC Symbol;Acc:18683] EIF4A2 eukaryotic translation initiation factor 4A2 [Source:HGNC Symbol;Acc:3284] D3/D0 0.993846591 D3/D0 -2.381425 opposite sign one paralog ENSMUSP00000101860 ENSMUSP00000023599 ENSG00000141543 ENSG00000156976
embl_complex_039; embl_complex_113 HDAC3/NCOR complex, GST-Smad3 NCOR2 nuclear receptor corepressor 2 [Source:HGNC Symbol;Acc:7673] NCOR1 nuclear receptor corepressor 1 [Source:HGNC Symbol;Acc:7672] D3/D0 -1.0696875 D3/D0 1.016145833 opposite sign none ENSMUSP00000107029 ENSMUSP00000018645 ENSG00000196498 ENSG00000141027
embl_complex_137 ISW1b complex HDGFRP3 Hepatoma-derived growth factor-related protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9Y3E1] HDGFRP2 Hepatoma-derived growth factor-related protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q7Z4V5] iPS/D12 -0.90835 iPS/D12 1.4036 opposite sign one paralog ENSMUSP00000102926 ENSMUSP00000002911 ENSG00000166503 ENSG00000167674
embl_complex_113 Mob1p/Dbf2p complex MOB2 MOB kinase activator 2 [Source:HGNC Symbol;Acc:24904] MOB3A MOB kinase activator 3A [Source:HGNC Symbol;Acc:29802] D3/D0 0.7424 D3/D0 -1.54885 opposite sign NA ENSMUSP00000081455 ENSMUSP00000003438 ENSG00000182208 ENSG00000172081
embl_complex_196 Nonsense-mediated mRNA decay pathway complex AQR aquarius intron-binding spliceosomal factor [Source:HGNC Symbol;Acc:29513] ZNFX1 zinc finger, NFX1-type containing 1 [Source:HGNC Symbol;Acc:29271] D3/D0 1.19425 D3/D0 -1.7198125 opposite sign one paralog ENSMUSP00000099602 ENSMUSP00000049404 ENSG00000021776 ENSG00000124201
embl_complex_208 RNA polymerase II complex chromatin structure modifying BAZ1A bromodomain adjacent to zinc finger domain, 1A [Source:HGNC Symbol;Acc:960] BAZ1B bromodomain adjacent to zinc finger domain, 1B [Source:HGNC Symbol;Acc:961] D3/D0 -2.3473125 D3/D0 0.829375 opposite sign NA ENSMUSP00000039757 ENSMUSP00000002825 ENSG00000198604 ENSG00000009954
embl_complex_264 Septin complex SEPT8 septin 8 [Source:HGNC Symbol;Acc:16511] SEPT9 septin 9 [Source:HGNC Symbol;Acc:7323] iPS/D12 2.54409375 iPS/D12 -1.24871875 opposite sign none ENSMUSP00000124057 ENSMUSP00000091435 ENSG00000164402 ENSG00000184640
embl_complex_069 smc5p-Smc6p complex NDNL2 necdin-like 2 [Source:HGNC Symbol;Acc:7677] MAGED1 melanoma antigen family D, 1 [Source:HGNC Symbol;Acc:6813] D3/D0 0.711625 D3/D0 -2.13415625 opposite sign one paralog ENSMUSP00000091889 ENSMUSP00000026142 ENSG00000185115 ENSG00000179222
embl_complex_090 SNARE complex VAMP4 vesicle-associated membrane protein 4 [Source:HGNC Symbol;Acc:12645] VAMP8 vesicle-associated membrane protein 8 [Source:HGNC Symbol;Acc:12647] D3/D0 1.56065625 D3/D0 -1.9329375 opposite sign none ENSMUSP00000114172 ENSMUSP00000059501 ENSG00000117533 ENSG00000118640
embl_complex_090 SNARE complex VAMP8 vesicle-associated membrane protein 8 [Source:HGNC Symbol;Acc:12647] VAMP3 vesicle-associated membrane protein 3 [Source:HGNC Symbol;Acc:12644] D3/D0 -1.9329375 D3/D0 0.68846875 opposite sign none ENSMUSP00000059501 ENSMUSP00000030797 ENSG00000118640 ENSG00000049245
embl_complex_071 INO80.com ACTB actin, beta [Source:HGNC Symbol;Acc:132] ACTBL2 actin, beta-like 2 [Source:HGNC Symbol;Acc:17780] D3/D0 -2.713193452 D3/D0 -2.516958333 same sign NA ENSMUSP00000130611 ENSMUSP00000052086 ENSG00000075624 ENSG00000169067
embl_complex_211 Kinase maturation complex 1 YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta [Source:HGNC Symbol;Acc:12853] YWHAB tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta [Source:HGNC Symbol;Acc:12849] D3/D0 -0.756951923 D3/D0 -0.940428285 same sign NA ENSMUSP00000019109 ENSMUSP00000018470 ENSG00000128245 ENSG00000166913
embl_complex_213 Kinase maturation complex 1 YWHAG tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma [Source:HGNC Symbol;Acc:12852] YWHAB tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta [Source:HGNC Symbol;Acc:12849] D3/D0 -0.894125 D3/D0 -0.940428285 same sign NA ENSMUSP00000051223 ENSMUSP00000018470 ENSG00000170027 ENSG00000166913
embl_complex_211 Kinase maturation complex 1 YWHAG tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma [Source:HGNC Symbol;Acc:12852] YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta [Source:HGNC Symbol;Acc:12853] D3/D0 -0.894125 D3/D0 -0.756951923 same sign NA ENSMUSP00000051223 ENSMUSP00000019109 ENSG00000170027 ENSG00000128245
embl_complex_233 RalBP1-CCNB1-AP2A-NUMB-EPN1 complex AP2A1 adaptor-related protein complex 2, alpha 1 subunit [Source:HGNC Symbol;Acc:561] AP2A2 adaptor-related protein complex 2, alpha 2 subunit [Source:HGNC Symbol;Acc:562] D3/D0 -1.456375 D3/D0 -1.182625 same sign NA ENSMUSP00000127842 ENSMUSP00000003038 ENSG00000196961 ENSG00000183020
embl_complex_075 RSC HSPA2 heat shock 70kDa protein 2 [Source:HGNC Symbol;Acc:5235] HSPA5 heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) [Source:HGNC Symbol;Acc:5238] D3/D0 -1.882636458 D3/D0 -1.893714815 same sign NA ENSMUSP00000079306 ENSMUSP00000028222 ENSG00000126803 ENSG00000044574
embl_complex_090 SNARE complex VAMP4 vesicle-associated membrane protein 4 [Source:HGNC Symbol;Acc:12645] VAMP3 vesicle-associated membrane protein 3 [Source:HGNC Symbol;Acc:12644] D3/D0 1.56065625 D3/D0 0.68846875 same sign NA ENSMUSP00000114172 ENSMUSP00000030797 ENSG00000117533 ENSG00000049245