Table S4. Statistics of quantified protein complexes
Complex IDComplex name# of sig. subunits in reprogramming# of quantified subunits in reprogrammingRatio of sig. subunits in reprogramming# of sig. subunits in 11 cell lines# of quantified subunits in 11 cell linesRatio of sig. subunits in 11 cell linesVariable complexes (>=0.2)
embl_complex_001 26S Proteasome 6 34 0.18 3 32 0.09 0.14
embl_complex_002 Nuclear pore complex (NPC) 6 28 0.21 6 27 0.22 0.22
embl_complex_003 Mediator 2 15 0.13 2 8 0.25 0.19
embl_complex_004 BAF complex 8 16 0.50 2 10 0.20 0.35
embl_complex_005 Integrator 1 14 0.07 0 12 0.00 0.04
embl_complex_006 Spliceosome-A 1 16 0.06 3 13 0.23 0.15
embl_complex_007 Large Drosha complex 2 17 0.12 2 16 0.13 0.12
embl_complex_008 Survival of motor neuron (SMN) complex 2 12 0.17 3 12 0.25 0.21
embl_complex_009 Polycomb-group repressive complex 1 (PRC1) 0 5 0.00 NA NA NA 0.00
embl_complex_010 Spliceosome-C 0 10 0.00 3 8 0.38 0.19
embl_complex_011 TAF complex 0 7 0.00 NA NA NA 0.00
embl_complex_012 Exon Junction Complex (EJC) 6 12 0.50 2 10 0.20 0.35
embl_complex_013 SIN3 complex 1 6 0.17 NA NA NA 0.17
embl_complex_015 NuRD complex 5 11 0.45 0 9 0.00 0.23
embl_complex_016 CCR4-NOT complex 1 12 0.08 2 6 0.33 0.21
embl_complex_017 INO80 complex 1 5 0.20 NA NA NA 0.20
embl_complex_018 Spliceosome-U2 2 9 0.22 0 12 0.00 0.11
embl_complex_019 STAGA complex 1 5 0.20 NA NA NA 0.20
embl_complex_020 Exosome 0 8 0.00 0 10 0.00 0.00
embl_complex_021 Polycomb-group repressive complex 2 (PRC2) 0 7 0.00 0 5 0.00 0.00
embl_complex_022 KMT2C/D containing complex 1 8 0.13 1 5 0.20 0.16
embl_complex_023 Anaphase promoting complex (APC) 1 8 0.13 1 7 0.14 0.13
embl_complex_025 Cohesin complex 1 8 0.13 2 8 0.25 0.19
embl_complex_026 Spliceosome-B 4 9 0.44 5 10 0.50 0.47
embl_complex_027 Transcription-export (TREX) complex 2 8 0.25 2 8 0.25 0.25
embl_complex_028 multi-tRNAsynthase complex 7 10 0.70 3 10 0.30 0.50
embl_complex_029 RANBP9-containing complex 2 6 0.33 1 6 0.17 0.25
embl_complex_030 NuA4/Tip60 HAT complex 4 7 0.57 0 7 0.00 0.29
embl_complex_031 RNA polymerase III core complex 0 6 0.00 NA NA NA 0.00
embl_complex_032 Spliceosome-Bact 0 7 0.00 3 7 0.43 0.21
embl_complex_033 Spliceosome-Prp19 0 8 0.00 1 8 0.13 0.06
embl_complex_034 COREST complex 0 6 0.00 NA NA NA 0.00
embl_complex_035 RNA polymerase II core complex 1 9 0.11 0 6 0.00 0.06
embl_complex_036 COP9 signalosome 0 9 0.00 1 8 0.13 0.06
embl_complex_037 TFIIH complex 0 5 0.00 NA NA NA 0.00
embl_complex_038 Spliceosome-U5 0 8 0.00 1 7 0.14 0.07
embl_complex_039 HDAC3/NCOR complex 4 5 0.80 NA NA NA 0.80
embl_complex_040 MCM complex 3 7 0.43 4 5 0.80 0.61
embl_complex_041 Nuclear cap binding complex (NCBC) 2 5 0.40 2 7 0.29 0.34
embl_complex_042 RNA polymerase I core complex 0 6 0.00 0 5 0.00 0.00
embl_complex_043 Spliceosome-LSm 0 5 0.00 0 6 0.00 0.00
embl_complex_044 Spliceosome-Sm 0 6 0.00 1 7 0.14 0.07
embl_complex_045 Rap1 complex 3 7 0.43 4 7 0.57 0.50
embl_complex_052 Mis12 centromere complex 3 5 0.60 NA NA NA 0.60
embl_complex_053 Toposome 2 5 0.40 4 6 0.67 0.53
embl_complex_055 SRC-3 complex 1 5 0.20 NA NA NA 0.20
embl_complex_056 Spliceosome-U4/U6 0 5 0.00 3 5 0.60 0.30
embl_complex_057 Signal recognition particle (SRP) complex 0 5 0.00 0 5 0.00 0.00
embl_complex_058 TFIIIC complex 0 5 0.00 0 5 0.00 0.00
embl_complex_059 Paf complex 0 5 0.00 0 5 0.00 0.00
embl_complex_060 Replication factor C (RFC) complex NA NA NA 0 5 0.00 0.00
embl_complex_062 Cleavage and polyadenylation specificity factor (CPSF) complex NA NA NA 1 5 0.20 0.20
embl_complex_064 Origin recognition complex (ORC) complex 3 5 0.60 NA NA NA 0.60
embl_complex_065 cytoplasmic ribosomal large subunit 5 42 0.12 1 44 0.02 0.07
embl_complex_066 cytoplasmic ribosomal small subunit 3 29 0.10 2 32 0.06 0.08
embl_complex_067 mitochondrial ribosomal large subunit 4 32 0.13 2 26 0.08 0.10
embl_complex_068 Nucleosomal protein complex 0 6 0.00 NA NA NA 0.00
embl_complex_069 smc5p-Smc6p complex 2 5 0.40 1 6 0.17 0.28
embl_complex_070 COPII 7 18 0.39 6 15 0.40 0.39
embl_complex_071 INO80.com 6 10 0.60 2 6 0.33 0.47
embl_complex_072 Yph1-L 1 16 0.06 6 19 0.32 0.19
embl_complex_073 mitochondrial ribosomal small subunit 8 19 0.42 3 17 0.18 0.30
embl_complex_074 H+-transporting ATPase, vacuolar 0 11 0.00 0 9 0.00 0.00
embl_complex_075 RSC 11 16 0.69 5 13 0.38 0.54
embl_complex_076 H3.3 com 5 14 0.36 6 12 0.50 0.43
embl_complex_077 ELL.com 1 12 0.08 1 8 0.13 0.10
embl_complex_078 AF4.com 1 12 0.08 3 10 0.30 0.19
embl_complex_079 Tubulins 1 8 0.13 NA NA NA 0.13
embl_complex_080 mRNA cleavage factor complex (CFI) 1 15 0.07 3 14 0.21 0.14
embl_complex_081 emerin C52 6 14 0.43 5 14 0.36 0.39
embl_complex_082 F0/F1 ATP synthase (complex V) 0 10 0.00 0 8 0.00 0.00
embl_complex_083 HCF-1N 3 16 0.19 5 14 0.36 0.27
embl_complex_084 CtBP 2 10 0.20 1 5 0.20 0.20
embl_complex_085 Rpd3L complex 3 8 0.38 2 6 0.33 0.35
embl_complex_086 COMPASS complex 1 11 0.09 1 9 0.11 0.10
embl_complex_087 heterotrimeric G-protein complex 1 6 0.17 NA NA NA 0.17
embl_complex_088 emerin C32 7 12 0.58 4 10 0.40 0.49
embl_complex_089 Sin3-CI 5 12 0.42 2 10 0.20 0.31
embl_complex_090 SNARE complex 3 5 0.60 NA NA NA 0.60
embl_complex_091 HMC Complex 5 9 0.56 4 8 0.50 0.53
embl_complex_092 emerin C25 3 12 0.25 2 12 0.17 0.21
embl_complex_093 E2F6.com-1 0 7 0.00 NA NA NA 0.00
embl_complex_094 telomerase 2 9 0.22 2 10 0.20 0.21
embl_complex_095 STE5-MAPK complex 0 6 0.00 NA NA NA 0.00
embl_complex_096 Cytochrome c oxidase (complex IV) 0 5 0.00 0 6 0.00 0.00
embl_complex_098 eIF3 1 10 0.10 2 10 0.20 0.15
embl_complex_099 Arp2/3 protein complex 1 9 0.11 1 7 0.14 0.13
embl_complex_100 NuA3 histone acetyltransferase complex 0 6 0.00 NA NA NA 0.00
embl_complex_101 Kornberg's mediator (SRB) complex 0 5 0.00 NA NA NA 0.00
embl_complex_102 mitochondrial pyruvate dehydrogenase complex 0 6 0.00 1 5 0.20 0.10
embl_complex_103 COPI 3 9 0.33 2 8 0.25 0.29
embl_complex_104 Cdc28p/Clb5p complex 2 5 0.40 NA NA NA 0.40
embl_complex_105 Sro1p/Sec4p/Sec9p complex 2 5 0.40 NA NA NA 0.40
embl_complex_106 chaperonin-containing T-complex 0 8 0.00 0 8 0.00 0.00
embl_complex_107 AP-1 adaptor complex 2 6 0.33 1 6 0.17 0.25
embl_complex_109 TRAPP complex 1 5 0.20 NA NA NA 0.20
embl_complex_110 multi-eIF complex 2 8 0.25 2 8 0.25 0.25
embl_complex_112 Mob1p/Dbf2p complex 4 6 0.67 NA NA NA 0.67
embl_complex_113 GST-Smad3 5 9 0.56 NA NA NA 0.56
embl_complex_114 BRCA1/BARD1 2 6 0.33 NA NA NA 0.33
embl_complex_115 Cytochrome bc1 complex (Ubiquinol-cytochrome c reductase complex, complex III) 0 9 0.00 0 9 0.00 0.00
embl_complex_116 protein phosphatase type 2A complex (Rts1p) 1 6 0.17 1 6 0.17 0.17
embl_complex_118 N-CoR-1 5 9 0.56 1 5 0.20 0.38
embl_complex_119 Exocyst complex 4 8 0.50 0 6 0.00 0.25
embl_complex_120 SRCAP 2 6 0.33 1 6 0.17 0.25
embl_complex_122 eIF4F 2 6 0.33 0 5 0.00 0.17
embl_complex_123 PFD-like 3 7 0.43 2 6 0.33 0.38
embl_complex_124 mitochondrial inner membrane presequence translocase complex 0 5 0.00 0 5 0.00 0.00
embl_complex_125 oligosaccharyl transferase complex 2 7 0.29 1 6 0.17 0.23
embl_complex_126 emerin 4 8 0.50 NA NA NA 0.50
embl_complex_128 ESCRT III complex 0 5 0.00 NA NA NA 0.00
embl_complex_129 Suv39h1 3 7 0.43 NA NA NA 0.43
embl_complex_130 NSL 1 5 0.20 NA NA NA 0.20
embl_complex_131 cAMP-dependent protein kinase 2 5 0.40 NA NA NA 0.40
embl_complex_132 BCOR 0 5 0.00 NA NA NA 0.00
embl_complex_134 BLM-CII 0 5 0.00 NA NA NA 0.00
embl_complex_136 ISW1b complex 4 6 0.67 NA NA NA 0.67
embl_complex_139 B-WICH 5 6 0.83 3 6 0.50 0.67
embl_complex_140 AP-3 adaptor complex 2 7 0.29 NA NA NA 0.29
embl_complex_141 Cul3p-RING ubiquitin ligase complex 2 5 0.40 NA NA NA 0.40
embl_complex_142 Flag-FCP1 1 7 0.14 1 7 0.14 0.14
embl_complex_144 Pol epsilon 2 5 0.40 NA NA NA 0.40
embl_complex_147 DNMT3B 1 6 0.17 4 5 0.80 0.48
embl_complex_148 Prp19-associated complex 0 5 0.00 0 6 0.00 0.00
embl_complex_151 mitochondrial outer membrane translocase complex 0 5 0.00 NA NA NA 0.00
embl_complex_152 MMS22L-TONSL NA NA NA 5 5 1.00 1.00
embl_complex_153 PAM complex 0 5 0.00 NA NA NA 0.00
embl_complex_154 emerin C24 3 7 0.43 5 6 0.83 0.63
embl_complex_156 HOPS complex 0 7 0.00 0 5 0.00 0.00
embl_complex_157 retromer complex 2 7 0.29 2 6 0.33 0.31
embl_complex_158 chromatin assembly complex 3 6 0.50 NA NA NA 0.50
embl_complex_160 SCF-CDC4 complex 0 6 0.00 4 5 0.80 0.40
embl_complex_162 UTP C complex NA NA NA 2 5 0.40 0.40
embl_complex_167 chromatin accessibility complex 3 5 0.60 NA NA NA 0.60
embl_complex_168 RNA Degradation Complex NA NA NA 3 5 0.60 0.60
embl_complex_169 HDAC1-PP1 2 5 0.40 0 5 0.00 0.20
embl_complex_173 UTP B complex 0 6 0.00 4 6 0.67 0.33
embl_complex_177 prefoldin complex 0 5 0.00 0 6 0.00 0.00
embl_complex_182 nuclear condensin complex 0 5 0.00 NA NA NA 0.00
embl_complex_185 UTP A complex NA NA NA 1 5 0.20 0.20
embl_complex_196 Nonsense-mediated mRNA decay pathway complex 2 5 0.40 NA NA NA 0.40
embl_complex_200 eIF2B 0 5 0.00 NA NA NA 0.00
embl_complex_202 Elongator complex 0 5 0.00 3 5 0.60 0.30
embl_complex_208 RNA polymerase II complex, chromatin structure modifying 7 16 0.44 4 11 0.36 0.40
embl_complex_209 TNF-alpha/Nf-kappa B signaling complex (RPL6, RPL30, RPS13, CHUK, DDX3X, NFKB2, NFKBIB, REL, IKBKG, NFKB1, MAP3K8, RELB, GLG1, NFKBIA, RELA, TNIP2, GTF2I) 2 10 0.20 3 9 0.33 0.27
embl_complex_210 CF IIAm complex (Cleavage factor IIAm complex) 1 13 0.08 2 13 0.15 0.12
embl_complex_211 Kinase maturation complex 1 6 14 0.43 2 12 0.17 0.30
embl_complex_212 TNF-alpha/NF-kappa B signaling complex 6 4 13 0.31 1 13 0.08 0.19
embl_complex_213 RC complex during S-phase of cell cycle 1 10 0.10 6 10 0.60 0.35
embl_complex_214 H2AX complex, isolated from cells without IR exposure 5 10 0.50 5 12 0.42 0.46
embl_complex_215 HES1 promoter-Notch enhancer complex 3 10 0.30 2 8 0.25 0.28
embl_complex_216 TNF-alpha/NF-kappa B signaling complex (CHUK, BTRC, NFKB2, PPP6C, REL, CUL1, IKBKE, SAPS2, SAPS1, ANKRD28, RELA, SKP1) 4 8 0.50 4 6 0.67 0.58
embl_complex_217 P2X7 receptor signalling complex 3 7 0.43 2 5 0.40 0.41
embl_complex_218 BLOC1-BLOC2 complex 0 5 0.00 NA NA NA 0.00
embl_complex_219 NK-3-Groucho-HIPK2-SIN3A-RbpA48-HDAC1 complex 1 5 0.20 NA NA NA 0.20
embl_complex_220 Polycystin-1 multiprotein complex (ACTN1, CDH1, SRC, JUP, VCL, CTNNB1, PXN, BCAR1, PKD1, PTK2, TLN1) 4 9 0.44 NA NA NA 0.44
embl_complex_221 SMN-PolII-RHA complex 2 9 0.22 0 6 0.00 0.11
embl_complex_222 RICH1/AMOT polarity complex, Flag-Rich1 precipitated 4 8 0.50 2 5 0.40 0.45
embl_complex_223 Emerin regulatory complex 4 7 0.57 NA NA NA 0.57
embl_complex_224 Conserved oligomeric Golgi (COG) complex 1 7 0.14 0 8 0.00 0.07
embl_complex_225 p27-cyclinE-Cdk2 - Ubiquitin E3 ligase (SKP1A, SKP2, CUL1, CKS1B, RBX1) complex 0 6 0.00 NA NA NA 0.00
embl_complex_226 DNA-PK-Ku-eIF2-NF90-NF45 complex 3 8 0.38 4 8 0.50 0.44
embl_complex_227 Kinase maturation complex 2 2 6 0.33 0 5 0.00 0.17
embl_complex_228 TNF-alpha/NF-kappa B signaling complex 7 3 5 0.60 2 5 0.40 0.50
embl_complex_229 ASF1-histone containing complex 3 5 0.60 NA NA NA 0.60
embl_complex_231 Respiratory chain complex I (early intermediate NDUFAF1 assembly), mitochondrial 1 6 0.17 1 5 0.20 0.18
embl_complex_233 RalBP1-CCNB1-AP2A-NUMB-EPN1 complex 3 5 0.60 NA NA NA 0.60
embl_complex_234 WIP-WASp-actin-myosin-IIa complex 2 5 0.40 NA NA NA 0.40
embl_complex_238 MDC1-MRN-ATM-FANCD2 complex 1 5 0.20 3 5 0.60 0.40
embl_complex_244 Ubiquilin-proteasome complex 1 6 0.17 NA NA NA 0.17
embl_complex_245 TRBP containing complex (DICER, TRBP, AGO2, RPL7A, EIF6, MOV10) NA NA NA 2 5 0.40 0.40
embl_complex_248 Wave-2 complex 0 5 0.00 NA NA NA 0.00
embl_complex_254 PCNA-MutS-alpha-MutL-alpha-DNA complex 0 5 0.00 NA NA NA 0.00
embl_complex_255 Decapping complex 2 5 0.40 NA NA NA 0.40
embl_complex_257 SMG-1-Upf1-eRF1-eRF3 complex (SURF) 0 5 0.00 NA NA NA 0.00
embl_complex_260 CRM1-RAN-PHAX-CBC complex (cap binding complex) 1 5 0.20 2 5 0.40 0.30
embl_complex_261 RNA pol II containing coactivator complex Tat-SF 1 5 0.20 1 5 0.20 0.20
embl_complex_263 SRm160/300 complex 0 5 0.00 1 5 0.20 0.10
embl_complex_264 Septin complex 2 5 0.40 NA NA NA 0.40
embl_complex_266 BARD1-BRCA1-CSTF complex 0 5 0.00 NA NA NA 0.00
embl_complex_272 SWI/SNF chromatin-remodeling complex 2 5 0.40 1 5 0.20 0.30
embl_complex_274 53BP1-containing complex 1 5 0.20 4 5 0.80 0.50