[No authors listed]
Mapping protein-protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein-protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24,540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein-protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations.
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PDCD6IP, CHAF1A, PARP3, RANBP9, SMC4, UBA2, SAE1, ARPC5, ARPC4, ARPC3, ARPC1B, ACTR3, ACTR2, ARPC2, RAD50, RASGRP1, LRPPRC, PDIA6, G3BP1, TRIM28, CDK2, CDK4, PSME3, CDK6, PSMD14, HNRNPR, SRRM1, DENND4A, SF3B4, LOC400927-CSNK1E, SAP18, SMNDC1, BCAS2, EIF1B, SF3A1, CDKN2A, BCKDK, PAK4, CDKN2C, CDO1, YAP1, CD2BP2, UBAC1, MCRS1, BAIAP2, PFDN6, EIF3M, SYNCRIP, STK25, MYBBP1A, HYOU1, NOP56, SSSCA1, GLRX3, ARPC1A, SPTLC1, SORBS1, SMC2, PRPF8, AHSA1, PAICS, MYL12A, ATP5L, NPRL2, IGF2BP1, IGF2BP3, IGF2BP2, PMVK, PNMA2, USP39, AP4B1, POLQ, CFL1, NUDC, PTGES3, MAP3K2, GIPC1, SRSF10, NEK6, NCKAP1, IQGAP2, MTHFD2, SDCCAG3, CLPX, RUVBL2, PGRMC1, RAB10, MALT1, RNPS1, MORF4L1, KDELR1, SF3A3, SERINC3, STIP1, ACOT2, EBNA1BP2, YWHAQ, GCN1, SF3B2, SLC27A4, TLK2, KDELR2, DSTN, NUDT21, CHD1, CPSF6, WDR5, HNRNPUL1, KPTN, CDC37, PKIG, CORO1A, PTP4A3, FAM107A, STRAP, ZNF277, AKAP13, AKAP11, DDX20, RPL35, RASSF8, SEC63, PDCD10, DDX19B, CYP4F8, PNKP, PHB2, TUSC2, GABARAP, U2AF2, TWF2, GABARAPL2, KCTD12, CIRBP, KLHDC3, DCD, FTSJ3, AP1S1, AP2S1, CLK2, CLK3, CLN5, CLTC, FRMD6, LSM12, LOXHD1, C19orf70, ALDH16A1, IRGQ, HIST2H3C, CNTF, COX4I1, COX5B, COX6B1, CMBL, AFAP1L1, COX6C, MTPN, NEK7, DYNLL2, SREK1, E2F7, CSNK1D, CSNK1E, CSNK2A1, CSNK2A2, CSNK2B, TTBK2, CDAN1, CSTB, KLC3, CSTF3, SLC30A7, CTNNB1, CTPS1, CBWD2, SGO2, PPP4R2, CREBRF, CYP1B1, CLEC2L, AMOTL1, C9orf163, DGKB, DBT, AP2B1, DCTN1, DDOST, DDT, DDX3X, DDX5, DDX6, DHX9, AES, DFFA, DFFB, TIMM8A, DHX36, DHCR7, DHPS, DLG3, DNASE2, DYNC1H1, DYNC1I2, DSG1, DSP, DYRK1A, TOR1A, ECHS1, AHCY, EEF1A2, EEF1B2, EEF1D, EIF2D, KRT78, EIF2S1, EIF2B1, EIF2S3, MLKL, EIF4A1, EIF4A2, EIF4E, EIF4EBP1, EIF4G1, EIF4G2, ELF3, TXLNA, CRTC2, MARK2, CMYA5, ENSA, AK1, EPB41, EPB41L2, STOM, EPO, EPRS, ERH, FBL, EWSR1, EXT1, EXT2, FABP4, FABP5, FANCC, FBLN1, CCNY, HNRNPA3, JMJD1C, FOXK1, FDFT1, FES, COPG1, HSPA4L, PUF60, CEP162, RAB11FIP2, CNKSR2, FKBP4, SIRT2, DKK1, ACIN1, RIMS1, STK38L, CNOT1, SNRNP200, SAMD4A, XPO7, PDXDC1, PDS5B, EMC1, ERP44, MYCBP2, ERC1, KIF1B, CDK19, AKR1B1, CLASP2, GPATCH8, EPB41L3, MAST2, SEPT6, MPRIP, NUP205, RTF1, FAM175B, METAP1, SEPT8, PASK, ATG4B, GANAB, FAF2, XPO6, RRP12, PDS5A, BOP1, NUP160, FBXW11, ANKS1A, KIAA0930, CLASP1, UBR4, LARP1, UFL1, SRGAP2, FNTA, KIAA0368, CRB1, FNTB, SF3B3, SF3B1, SEC11A, PES1, NUP188, SKIV2L2, SRRM2, TNPO3, DNPEP, GTPBP4, KLHDC2, PHLDA3, KPNA6, SH3BP4, KIF4A, EML2, PRPF6, CNOT6L, ALPI, FUS, MMS22L, EBF3, EML3, SUN2, DSTYK, RASGRP3, RAB3GAP2, RAD54B, LSM4, ATXN10, TNFAIP8, MOB4, RPL36, MTHFD1L, CNOT10, DPCD, NELFB, ASPM, GAPDH, CHMP2B, HIGD1A, IBTK, RNF167, OSBPL3, RAI14, KIF1BP, GAPVD1, SERBP1, NOC2L, RSL1D1, PCDHB5, TIPRL, GART, GAS8, TSPAN17, FBXO4, EHF, GBAS, GAPDHS, GNL3, CNNM4, CNNM3, TIMM13, TIMM8B, OSTF1, GDI1, NAP1L5, AMFR, GH1, COPG2, PABPC1, AKAP8L, SND1, CACYBP, STK36, GLB1, PDCD4, GCLM, RBMX, EIF3K, HTATSF1, PRPF19, RABGEF1, APOBEC3C, EML4, AMY1A, AMY1B, GNAS, AMY1C, GOT2, FAM98B, TMEM102, FRYL, RPL7L1, GPS1, GPS2, GIT1, BZW2, MRPS18B, DBNL, CCDC59, BABAM1, CNIH4, CFAP20, RACGAP1, GSK3A, GSK3B, GSN, GSTM3, MSH6, GTF2A1, GTF2A2, GTF2I, PACSIN3, PARVB, OLA1, STRN4, GNL2, SEC61A1, CERS2, NRBP1, STRN3, GYS1, TNPO2, ANXA1, ANXA2, HADHA, HAS1, HBG1, HDLBP, HELLS, KCNIP2, EHD4, PIK3R4, UBE2K, HLA-A, HLA-B, ACACA, HNF4A, HNRNPAB, HNRNPC, HNRNPH3, HNRNPL, HPRT1, PRMT1, DNAJA1, HSPB1, BIRC5, HSPE1, HIST2H3A, HTR1B, HTR1E, HUS1, IARS, KRTAP19-5, ICA1, PKD1L3, APOD, IGF1R, IGHA1, IGHA2, IGKC, APRT, BPIFB3, ILK, IMPDH2, EIF3E, ARAF, EIF6, JAK1, JUP, GSTK1, KRT77, KHK, KIF5B, KIF5C, ACAT1, ARF6, KLC1, KPNA1, KPNA3, KPNA4, KRT8, RHOA, KRT18, RPL21P97, KRT31, KRT32, KRT33A, KRT33B, KRT34, KRT35, HRNR, KRT82, KRT85, RHOC, ACAT2, LBR, LCN1, LGALS1, LGALS3BP, ARHGDIA, LGALS9, LIG3, LIG4, LIMS1, FADS1, ARL1, LTA4H, LTF, LYN, LYZ, ARR3, CAPRIN1, ARRB1, MAD2L1, ARRB2, MAGEA6, MAGEB2, MAGOH, MARK3, MARS, MAX, MCC, MCM3, MCM5, MCM7, RAB8A, MEN1, MEST, MET, MFAP1, MIF, MKLN1, MLLT4, MNAT1, MOV10, MPG, ALG11, RPL35P5, MYO1B, MSH2, MSN, COX2, NUDT1, MTHFD1, MTR, MTX1, MYC, MYH2, MYH4, MYH7, MYH9, MYH10, MYL6, MYO1C, MYO1D, MYO6, PPP1R12A, HNRNPM, NASP, NDN, NDUFA9, ATIC, ACLY, SEPT2, NEDD8, NFKBIL1, TONSL, NME2, ATP1B3, NPM1, ATP2A2, ATP2A3, NSF, NTHL1, NUP98, OAT, OAZ2, ODC1, OGG1, OPA1, ZBTB21, WRAP73, P4HB, PA2G4, PEBP1, PAK2, GEMIN4, PCBD1, RRP15, BOLA1, UBXN1, YARS2, DERA, MRPS7, PCMT1, NDUFAF1, KMT5B, ASB3, COPS4, TCEAL9, CHMP1A, IPO11, ACP6, VRK3, CDK17, HOOK1, UBR5, EIF3L, DDX41, HACD3, NELFCD, TRMT112, UFC1, CHMP5, ATP5F1, LARS, GSKIP, RAB14, HDAC7, UFM1, AZIN1, SRRT, LSR, PDHA1, METTL13, GET4, LUC7L2, SF3B6, TMBIM4, FAM96B, STYXL1, CAB39, DNAJB11, LUC7L3, INPP5K, CALML5, PFAS, PFDN1, PFDN2, PFKFB3, PFKP, ACP1, CDK14, PHYH, PIGR, PIK3C3, PIK3R1, PI4KB, PIN1, PIP, PITPNA, PLOD2, PLRG1, PLS3, PELO, CPSF2, PNN, CYCS, POLD1, POLE, POLR2A, POLR2B, POLR2H, KCTD5, PON2, CPVL, DDX56, ATRX, OTUD4, CTSA, PPIB, QPCTL, ERCC6L, SNRK, DNAAF5, SARS2, PPM1A, PPM1B, PINX1, GID8, PPP1CB, AUP1, PTCD3, PLEKHB2, PPP1R2, NRDE2, ATG16L1, SAMD4B, EBLN2, PPP1R7, RALGPS2, PLEKHJ1, PPP1R8, PRPF38B, HEATR1, SDAD1, TMEM33, PPP2CB, RMDN3, MRM3, PPP2R1A, PPP2R2A, ATAD3A, FANCI, NAT10, MOB1A, ASXL2, ADI1, BRF2, BRIX1, PPP4C, WDR33, LRRC59, CHST12, TTC27, SMPD4, PRKAB1, OSGEP, LYAR, PRKAB2, PRPF40A, DDX27, PRKACA, PPP4R3A, LUC7L, VAC14, RADIL, MAP7D1, IPO9, TSR1, ASF1B, PRKAR1A, VPS35, PARVA, NUP133, SEPT11, PCID2, ITFG2, CBWD1, UNC45A, BIN3, C20orf24, EIF2AK2, SUSD2, PARD3, PPAN, PRPSAP1, RPRM, BCCIP, BARHL1, PSMA1, PSMA2, PSMA3, PSMA6, PSMA7, UGGT1, PSMB1, SPIRE1, PSMB3, PAK6, LXN, PSMB5, MRPS22, SMYD2, CTNNBIP1, PSMC1, CCDC47, PSMC2, PSMC3, RARS2, PSMC4, PSMC5, PSMC6, DDX24, PSMD1, PSMD2, PSMD3, PARP11, PSMD4, RAB25, PSMD7, PSMD8, RTN4, PAK7, PSMD10, PSMD11, ACTR3B, PSMD12, PSMD13, PPP4R3B, PSPH, JPH3, PTK2, XPO5, CGN, LRRC7, UNC79, PREX1, VPS18, DHX37, ALS2, PTPN3, CCAR2, BAK1, PTPRS, PURA, ABCD3, PYGM, SRPRB, KMT2C, CACTIN, RBM25, RAB5A, RAB5C, RAC1, RAD51, RAD51D, RAF1, RANBP1, RANBP2, RANGAP1, RARS, RASGRF2, RBBP4, BCKDHA, RCN2, RFC4, RFC5, RGS2, RGS10, EXOC4, ELAC2, SMAP1, RPA3, RPL3, RPL18A, RPL21, RPL22, RPL23A, RPL24, RPL26, RPL28, RPL29, RPL31, RPL32, RPL34, RPL35A, RPL37, RPL37A, RPL38, RPL36A, RPN1, RPN2, RPS3A, RPS9, RPS10, RPS11, RPS14, RPS16, RPS19, RPS26, RPS28, RPS29, RRBP1, RSU1, SORT1, S100A3, S100A7, S100A8, S100A9, SARS, ATXN2, SERPINB3, SERPINB4, CCL14, RNF123, SH2D4A, MRPS14, CXorf56, NCAPG, SET, MMS19, SRSF1, SRSF2, SRSF3, RAB17, SRSF4, SRSF6, SRSF7, XPO4, SFSWAP, TRA2B, NXN, AKTIP, ATG3, POLR1E, MRPS25, NOM1, SGK1, FAM83G, SHMT2, SMYD3, PCED1A, ELOVL1, KLC2, CENPH, MRPS24, MRPS9, MRPS5, SKP1, CDK15, MRPL44, SLC1A5, SLC3A2, NADK, HIST2H3D, NME1-NME2, SLC16A1, SLC25A1, SMARCA4, SMARCC1, DDRGK1, MRPS34, SMN2, SUMO3, SNAI1, SNCG, FSCN1, SNRNP70, SNRPA, SNRPA1, SNRPB, SNRPB2, SNRPF, SNRPG, SNRPN, SOD2, SON, SRP14, BRAF, SRPK1, SRPK2, TROVE2, SSB, SSR3, SSR4, STAT1, AURKA, STRN, BSG, SURF4, TAGLN, TARS, TCEB1, TCEB2, HNF1A, TCOF1, PPP1R11, TFE3, TGFB1I1, TGIF1, TCHH, TIAM1, TIMP2, TKT, TLE1, TLE3, TSPAN7, CLEC3B, TPM3, TPT1, TRAF2, TRAF6, TRIP6, TSC1, TSC2, TSSC1, TTC4, TTN, D2HGDH, TUFM, RPL36AP37, TXN, U2AF1, UBE2D3, UBE2G2, UBE2I, UBE2L3, SUMO1, UGP2, UQCRC1, UQCRC2, USF1, USF2, VARS, VCP, VDAC1, VDAC2, VDAC3, VHL, VIL1, EZR, WEE1, XRCC1, XRCC4, YWHAB, YWHAG, YWHAZ, CNBP, PTP4A1, DAP3, BTG2, SLMAP, USP7, RAB7A, BAG6, BRCC3, SLC39A7, NELFE, RNF219, ARMT1, CHMP6, LRRK1, IPO4, SLC25A22, CCDC82, SHCBP1, MOB3B, NAA25, PANK2, CALM1, EDC3, RAB11FIP1, PAAF1, CDK5RAP3, CCDC6, EFHD1, WDCP, KCNIP4, CALM2, CUL5, PTP4A2, MLF2, CALM3, SH3BP5L, KIAA1715, CDK2AP1, CALR, CAMK2A, CAB39L, CAMK2B, CAMK2D, ELL, ARPC5L, RAB1B, LAS1L, MKKS, CHAF1B, AKAP17A, USP11, USP9X, SMC1A, LAGE3, CAPZA1, TRRAP, CAPZA2, AXIN1, CAPZB, HIST1H2BC, EPPK1, HIST2H2BE, HIST1H3A, HIST1H3D, HIST1H3C, HIST1H3E, TTC25, NUF2, HIST1H3I, HIST1H3G, HIST1H3J, HIST1H3H, HIST1H3B, HSDL1, CASP4, ATG10, ATAD3B, KRTAP9-2, KRTAP9-3, PIP5K1B, NACAP1, SPOP, TAGLN2, MYCBPAP, QRICH2, ULK1, PCBD2, BCAR3, RPF2, FAR1, STK24, KIAA1804, NEURL4, FAM120B, C15orf41, CUL2, CUL1, MRPL43, TTBK1, HDGFRP2, OGT, GEMIN2, PPFIBP1, RANBP3, NIPSNAP1, DGKE, COPS3, STRIP1, BCAS1, MICALL1, RHPN2, AP3B1, DEGS1, YARS, KHSRP, PRKRA, STK16, RGS20, SLC25A12, RUVBL1, USO1, RUNX1T1, RFXANK, RTCA, RUNX3, DYNLL1, IRS2, EIF3A, EIF3D, EIF3F, EIF3G, EIF3H, EIF3I, EIF4G3, KRT36, ARPC3P1, GBF1, CBR1, PABPC4, TNFRSF14, RAB11A, RIPK2, RIOK3, TNFRSF10D, DPM1, IQGAP1, CFLAR, WISP1, HDAC3, TSC22D1, ASAP2, ARHGEF7, SQSTM1, FUBP1, NAE1, EIF2B3, EIF2B5, PRPF4B, CCNA1, BCL10, HERC2, HERC1, HIST1H3F, KLC4, NOL3, CCNH, UBA3, UBE2M, SPAG9, DOK2, PSTPIP1, PAPSS2, DHX57, USP8, SMC3, PRPF3, AIFM1, RABEP1, ATG12, FIBP, NEK9, ARHGEF2, ZW10, DDX21, DEDD, NOLC1, MAGI1, TBRG4, TIMM50, COPB2, SRSF11, COPS2, GTF3C3, CNOT8, TCEAL1, EFTUD2, ARMC6, UBE4A, PPIG, MRFAP1, COX5A, CIAO1, ZRANB2, SFXN1, SNRNP40, TJP2, DDX23, MED7, RASAL2, EIF4E2, ATG5, ROCK2, KIF23, SLC4A7, MAGED1, FXR2, TBPL1, NPEPPS, MPDU1, BAG2, POLR1C, BRE, CDC42BPB, CD40, PDIA4, ISG15, IKBKE, MORF4L2, CEP135, NUP93, BZW1, EDEM1, DOCK4, SART3, KNTC1, HDAC4, BCLAF1, MATR3, DHX38, GIT2, RB1CC1, ZBTB24, CDK11B, C2CD5, PSMD6, MAGI2, LRBA, TLK1, CDC5L, TBC1D4, NUAK1, SEPT7, TELO2, G3BP2, CDC20, CDC25B, OXSR1, USP15, THRAP3, RBX1, CDC42, HNRNPDL, PPP4R1
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