Table I List of differentially expressed proteins in PRA1-knockdown NPC cell clones identified both in Exp 1 and Exp 2
Accession No.Protein name (Gene name)ExperimentProteinProphet probabilityaNo. of identified peptidesPercent coverage (%)iTRAQ ratios (mean ± S.D.)bNo. of spectra for quantificationNo. of unique peptides for quantificationGO biological process categoryd
K3–8/C15c (116/114)K3–8/C15–3c (116/115)K3–14/C15c (117/114)K3–14/C15–3c (117/115)
Up-regulated proteins
    IPI00005102.3Spermine synthase (SMS)11.00414.51.18 ± 0.241.06 ± 0.161.50 ± 0.261.36 ± 0.19144spermine biosynthetic process
21.00510.41.19 ± 0.260.99 ± 0.201.54 ± 0.191.28 ± 0.17123
    IPI00007797.3Fatty acid-binding protein, epidermal (FABP5)11.00428.11.25 ± 0.241.57 ± 0.441.47 ± 0.341.84 ± 0.51154lipid metabolic process; epidermis development
21.00428.11.32 ± 0.301.58 ± 0.361.48 ± 0.261.78 ± 0.35114
    IPI00008475.1Hydroxymethylglutaryl-CoA synthase, cytoplasmic (HMGCS1)11.001126.51.43 ± 0.261.62 ± 0.330.93 ± 0.161.06 ± 0.217511cholesterol biosynthetic process
21.001328.81.30 ± 0.251.43 ± 0.340.90 ± 0.170.98 ± 0.18459
    IPI00008986.1Large neutral amino acids transporter small subunit 1 (SLC7A5)11.0038.31.66 ± 0.591.09 ± 0.081.55 ± 0.511.03 ± 0.08222amino acid transport
21.0027.31.57 ± 0.461.05 ± 0.121.59 ± 0.461.06 ± 0.15162
    IPI00009236.5Isoform Alpha of Caveolin-1 (CAV1)11.00328.11.25 ± 0.191.30 ± 0.171.28 ± 0.581.40 ± 0.5073cholesterol homeostasis; cholesterol transpor; endocytosis
21.00216.91.62 ± 0.441.68 ± 0.452.26 ± 0.472.35 ± 0.50142
    IPI00009943.2Tumor protein, translationally-controlled 1 (TPT1)11.00535.61.03 ± 0.211.45 ± 0.401.39 ± 0.261.99 ± 0.59355
21.00514.41.15 ± 0.211.34 ± 0.261.72 ± 0.551.99 ± 0.58132
    IPI00010214.1Protein S100-A14 (S100A14)11.00327.91.02 ± 0.301.23 ± 0.321.31 ± 0.381.57 ± 0.40282calcium ion binding; chemokine receptor binding
21.00226.01.14 ± 0.301.43 ± 0.381.44 ± 0.331.85 ± 0.6082
    IPI00010471.5Plastin-2 (LCP1)11.002052.61.06 ± 0.230.91 ± 0.121.60 ± 0.401.37 ± 0.2115719regulation of intracellular protein transport
21.002146.31.07 ± 0.260.97 ± 0.161.56 ± 0.481.36 ± 0.2616016
    IPI00010697.1Isoform Alpha-6X1X2B of Integrin alpha-6 precursor (ITGA6)11.0088.21.12 ± 0.311.24 ± 0.291.59 ± 0.461.76 ± 0.45237cell adhesion; integrin-mediated signaling pathway
21.00446.31.57 ± 0.321.51 ± 0.141.75 ± 0.481.66 ± 0.1893
    IPI00010860.1Isoform p27-L of 26S proteasome non-ATPase regulatory subunit 9 (PSMD9)11.00222.01.43 ± 0.311.45 ± 0.200.95 ± 0.210.97 ± 0.13122proteasomal ubiquitin-dependent protein catabolic process
21.0027.61.55 ± 0.411.65 ± 0.500.99 ± 0.211.04 ± 0.20122
    IPI00011126.626S protease regulatory subunit 4 (PSMC1)11.00835.21.33 ± 0.401.03 ± 0.231.38 ± 0.501.05 ± 0.19417proteasomal ubiquitin-dependent protein catabolic process
21.00932.01.50 ± 0.640.87 ± 0.201.91 ± 1.231.00 ± 0.16266
    IPI00011200.5d-3-phosphoglycerate dehydrogenase (PHGDH)11.00825.71.54 ± 0.411.05 ± 0.111.38 ± 0.390.94 ± 0.09718amino-acid biosynthesis
21.00721.01.44 ± 0.380.98 ± 0.121.34 ± 0.340.91 ± 0.09666
    IPI00011250.3Ubiquitin carboxyl-terminal hydrolase isozyme L3 (UCHL3)11.00546.11.06 ± 0.161.28 ± 0.291.42 ± 0.241.74 ± 0.52254ubiquitin-dependent protein catabolic process
21.00635.71.14 ± 0.391.21 ± 0.461.46 ± 0.531.55 ± 0.60215
    IPI00013890.2Isoform 1 of 14-3-3 protein sigma (SFN)11.00850.40.96 ± 0.121.11 ± 0.171.32 ± 0.201.54 ± 0.281757DNA damage response
21.001433.00.99 ± 0.171.02 ± 0.191.31 ± 0.271.34 ± 0.281468
    IPI00014197.2Protein CDV3 homolog (CDV3)10.9828.91.08 ± 0.081.60 ± 0.381.14 ± 0.201.70 ± 0.4892cell proliferation
21.00530.21.17 ± 0.321.40 ± 0.341.19 ± 0.291.44 ± 0.3463
    IPI00015117.2Isoform Long of Laminin subunit gamma-2 precursor (LAMC2)10.9923.11.21 ± 0.281.88 ± 0.401.19 ± 0.171.88 ± 0.4332cell adhesion; epidermis development
21.0023.11.23 ± 0.042.00 ± 0.381.28 ± 0.101.79 ± 0.2422
    IPI00016832.1Isoform Short of Proteasome subunit alpha type 1 (PSMA1)11.00948.31.70 ± 1.371.12 ± 0.251.34 ± 0.900.94 ± 0.17427proteasomal ubiquitin-dependent protein catabolic process
21.001027.01.85 ± 1.351.05 ± 0.201.53 ± 0.920.93 ± 0.19304
    IPI00017448.140S ribosomal protein S21 (RPS21)11.00454.21.66 ± 0.480.98 ± 0.091.58 ± 0.480.93 ± 0.08284translational elongation
21.00231.31.85 ± 0.440.96 ± 0.061.79 ± 0.450.92 ± 0.05132
    IPI00017450.2Transcription initiation factor IIF subunit alpha (GTF2F1)11.0049.71.38 ± 0.860.79 ± 0.131.65 ± 1.050.95 ± 0.0893transcription regulation
21.0037.41.26 ± 0.350.81 ± 0.121.42 ± 0.400.91 ± 0.08103
    IPI00017704.3Coactosin-like protein (COTL1)11.00450.51.57 ± 0.821.06 ± 0.201.42 ± 0.611.00 ± 0.13103actin binding; enzyme binding
21.00220.42.21 ± 0.201.07 ± 0.051.98 ± 0.120.97 ± 0.0551
    IPI00018219.1Transforming growth factor-beta-induced protein ig-h3 precursor (TGFBI)11.0023.80.93 ± 0.101.13 ± 0.211.77 ± 0.332.14 ± 0.4392cell adhesion; negative regulation of cell adhesion
21.0033.80.95 ± 0.160.94 ± 0.121.41 ± 0.191.76 ± 0.1641
    IPI00022078.3Protein NDRG1 (NDRG1)11.00218.30.93 ± 0.211.48 ± 0.201.78 ± 0.352.88 ± 0.61102response to metal ion
21.00520.30.87 ± 0.151.48 ± 0.311.71 ± 0.202.92 ± 0.56193
    IPI00024095.3Annexin A3 (ANXA3)11.00520.21.09 ± 0.151.08 ± 0.141.69 ± 0.271.67 ± 0.23314cell motion; signal transduction
21.00629.41.14 ± 0.161.02 ± 0.171.79 ± 0.261.60 ± 0.20343
    IPI00026087.1Barrier-to-autointegration factor (BANF1)11.00348.32.11 ± 0.990.72 ± 0.082.17 ± 0.830.80 ± 0.1983host-virus interaction
21.00340.41.30 ± 0.260.90 ± 0.101.44 ± 0.281.01 ± 0.1742
    IPI00026202.160S ribosomal protein L18a (RPL18A)11.00743.81.69 ± 1.440.91 ± 0.201.51 ± 1.260.82 ± 0.11277translational elongation
21.001334.71.63 ± 1.200.99 ± 0.231.39 ± 1.040.94 ± 0.14346
    IPI00026546.1Platelet-activating factor acetylhydrolase IB subunit beta (PAFAH1B2)11.00318.31.33 ± 0.260.94 ± 0.111.29 ± 0.160.92 ± 0.10202lipid catabolic process
21.00314.81.41 ± 0.250.86 ± 0.101.31 ± 0.130.81 ± 0.05182
    IPI00026813.1Protein farnesyltransferase/ geranylgeranyltransferase type I alpha subunit11.0026.10.97 ± 0.191.58 ± 0.711.08 ± 0.161.72 ± 0.5782protein amino acid farnesylation
21.00310.81.13 ± 0.281.33 ± 0.591.31 ± 0.211.51 ± 0.5672
    IPI00027422.1Isoform Beta-4C of Integrin beta-4 precursor (ITGB4)11.001112.71.38 ± 0.381.41 ± 0.221.56 ± 0.431.59 ± 0.23558cell-matrix adhesion; integrin-mediated signaling pathway
21.00108.61.39 ± 0.431.42 ± 0.261.64 ± 0.461.70 ± 0.31436
    IPI00027493.14F2 cell-surface antigen heavy chain (SLC3A2)11.001644.01.36 ± 0.471.16 ± 0.201.31 ± 0.421.12 ± 0.1813914calcium ion transport; amino-acid transport
21.002439.11.36 ± 0.521.09 ± 0.191.31 ± 0.491.05 ± 0.1514913
    IPI00028091.3Actin-like protein 3 (ACTR3)11.00626.31.26 ± 0.421.01 ± 0.241.45 ± 0.491.14 ± 0.22336cell motion; actin filament polymerization
21.00931.11.54 ± 0.620.96 ± 0.181.74 ± 0.701.08 ± 0.14315
    IPI00032849.2UPF0384 protein CGI-117 (NOP16)10.99319.71.20 ± 0.132.36 ± 1.950.90 ± 0.471.36 ± 0.4722
21.0028.41.10 ± 0.411.01 ± 0.571.68 ± 0.401.54 ± 0.5761
    IPI00062120.1Protein S100-A16 (S100A16)11.00333.01.12 ± 0.221.22 ± 0.321.40 ± 0.321.53 ± 0.43173calcium ion binding
21.00329.11.09 ± 0.291.10 ± 0.341.36 ± 0.411.44 ± 0.68151
    IPI00171856.1Deoxyhypusine hydroxylase (DOHH)11.00326.81.30 ± 0.351.17 ± 0.441.28 ± 0.161.15 ± 0.2763oxidation reduction
21.00326.81.64 ± 0.371.23 ± 0.391.33 ± 0.170.99 ± 0.1353
    IPI00218918.5Annexin A1 (ANXA1)11.001867.61.11 ± 0.201.34 ± 0.251.25 ± 0.231.51 ± 0.2622218cell motion; lipid metabolic process; anti-apoptosis
21.003465.91.10 ± 0.191.28 ± 0.301.24 ± 0.231.44 ± 0.3221617
    IPI00218993.1Isoform Beta of Heat-shock protein 105 kDa (HSPH1)11.002449.01.19 ± 0.291.31 ± 0.241.53 ± 0.401.68 ± 0.3418119stress response
21.003446.41.25 ± 0.281.24 ± 0.291.55 ± 0.371.54 ± 0.3715918
    IPI00219219.3Galectin-1 (LGALS1)11.00651.10.85 ± 0.140.97 ± 0.161.36 ± 0.261.55 ± 0.28476regulation of apoptosis
21.00843.70.97 ± 0.180.98 ± 0.211.30 ± 0.281.32 ± 0.33395
    IPI00219468.4Isoform IIa of Profilin-2 (PFN2)11.00335.71.04 ± 0.231.27 ± 0.211.77 ± 0.672.14 ± 0.65163actin cytoskeleton organization
20.99215.01.35 ± 0.151.41 ± 0.222.39 ± 0.162.51 ± 0.36101
    IPI00219953.5Cytidylate kinase (CMPK1)11.00220.21.40 ± 0.350.86 ± 0.131.54 ± 0.410.94 ± 0.09212pyrimidine biosynthesis
21.00212.31.62 ± 0.190.83 ± 0.091.88 ± 0.230.96 ± 0.07162
    IPI00220487.4Isoform 1 of ATP synthase D chain, mitochondrial (ATP5H)11.00324.21.22 ± 0.241.31 ± 0.301.65 ± 0.731.73 ± 0.7452ATP synthesis coupled proton transport
21.00324.21.25 ± 0.241.25 ± 0.301.71 ± 0.731.66 ± 0.7452
    IPI00303300.3FK506-binding protein 10 precursor (FKBP10)11.0024.50.98 ± 0.271.70 ± 0.431.65 ± 0.432.86 ± 0.5481protein folding
21.0044.50.87 ± 0.171.11 ± 0.231.71 ± 0.472.18 ± 0.6682
    IPI00303882.2Isoform B of Mannose-6-phosphate receptor-binding protein 1 (TIP47, PLIN3)11.00730.61.08 ± 0.320.93 ± 0.121.69 ± 0.631.45 ± 0.30336vesicle-mediated transport
21.00730.61.11 ± 0.310.99 ± 0.191.74 ± 0.621.42 ± 0.30346
    IPI00306369.3NOL1/NOP2/Sun domain family 2 protein (NSUN2)11.001336.01.40 ± 0.351.16 ± 0.181.32 ± 0.331.10 ± 0.173912tRNA methylation
21.001122.31.47 ± 0.311.09 ± 0.161.36 ± 0.301.01 ± 0.17408
    IPI00306960.3Asparaginyl-tRNA synthetase, cytoplasmic (NARS)11.0037.11.71 ± 0.650.89 ± 0.111.44 ± 0.420.77 ± 0.0483protein biosynthesis
21.00312.21.67 ± 0.310.91 ± 0.141.50 ± 0.400.94 ± 0.17103
    IPI00329629.6DnaJ homolog subfamily C member 7 (DNAJC7)11.0036.91.48 ± 0.391.33 ± 0.181.07 ± 0.260.97 ± 0.1283protein folding
21.0037.51.53 ± 0.601.23 ± 0.191.23 ± 0.321.03 ± 0.20103
    IPI00329801.12Annexin A5 (ANXA5)11.001557.20.92 ± 0.220.95 ± 0.171.56 ± 0.461.61 ± 0.3311515anti-apoptosis; blood coagulation
21.002552.80.92 ± 0.260.87 ± 0.181.57 ± 0.431.50 ± 0.3311314
    IPI00465184.3Guanine deaminase (GDA)11.0037.51.41 ± 0.361.49 ± 0.380.93 ± 0.201.00 ± 0.3263nucleic acid metabolic process
21.00210.81.76 ± 0.201.64 ± 0.331.09 ± 0.241.02 ± 0.2942
    IPI00465260.3Trifunctional purine biosynthetic protein adenosine-3 (GART)11.0049.11.00 ± 0.151.31 ± 0.231.12 ± 0.241.45 ± 0.27144purine biosynthesis
21.00811.71.09 ± 0.231.31 ± 0.301.29 ± 0.311.57 ± 0.52196
    IPI00470525.5Glycogen phosphorylase, liver form (PYGL)11.00814.81.16 ± 0.221.29 ± 0.331.30 ± 0.341.42 ± 0.29197glucose homeostasis; glycogen metabolic process
21.00915.51.24 ± 0.241.22 ± 0.231.41 ± 0.191.38 ± 0.19125
    IPI00472082.2Isoform 1 of Serpin B5 (SERPINB5)11.00728.91.03 ± 0.191.09 ± 0.161.49 ± 0.421.56 ± 0.30426protein binding
21.00925.71.04 ± 0.121.13 ± 0.161.38 ± 0.271.49 ± 0.29325
    IPI00554786.4Thioredoxin reductase 1, cytoplasmic precursor (TXNRD1)11.00318.41.46 ± 0.361.46 ± 0.261.03 ± 0.281.04 ± 0.21173cell redox homeostasis; electron transport
21.00616.61.65 ± 0.581.48 ± 0.491.18 ± 0.261.08 ± 0.32284
Down-regulated proteins
    IPI00000873.3Valyl-tRNA synthetase (VARS)11.0056.20.92 ± 0.330.68 ± 0.140.80 ± 0.170.60 ± 0.1274translational elongation
21.0087.00.78 ± 0.140.64 ± 0.090.82 ± 0.140.68 ± 0.13196
    IPI00011913.1Heterogeneous nuclear ribonucleoprotein A0 (HNRNPA0)11.00421.00.74 ± 0.120.72 ± 0.090.78 ± 0.140.77 ± 0.12174mRNA processing
21.00419.00.79 ± 0.080.71 ± 0.090.70 ± 0.100.63 ± 0.08222
    IPI00013495.1Isoform 2 of ATP-binding cassette sub-family F member 1 (ABCF1)11.0038.90.84 ± 0.130.81 ± 0.160.66 ± 0.120.63 ± 0.1273inflammatory response; translation
21.0045.10.85 ± 0.070.73 ± 0.100.74 ± 0.150.63 ± 0.12113
    IPI00013808.1Alpha-actinin-4 (ACTN4)11.00620.00.98 ± 0.160.69 ± 0.120.96 ± 0.130.68 ± 0.12245protein transport; regulation of apoptosis
21.00618.90.93 ± 0.150.58 ± 0.111.02 ± 0.150.64 ± 0.12144
    IPI00013871.1Ribonucleoside-diphosphate reductase large subunit (RRM1)11.00524.40.79 ± 0.160.73 ± 0.110.70 ± 0.250.65 ± 0.20155DNA replication; oxidation reduction
21.0026.60.93 ± 0.110.76 ± 0.260.78 ± 0.190.64 ± 0.2551
    IPI00015688.1Glypican-1 precursor (GPC1)11.00211.60.89 ± 0.090.66 ± 0.050.79 ± 0.140.58 ± 0.0121heparan sulfate proteoglycan binding
21.0029.31.02 ± 0.130.77 ± 0.120.95 ± 0.150.72 ± 0.1332
    IPI00018452.1Copine-1 (CPNE1)11.00615.80.81 ± 0.100.53 ± 0.101.06 ± 0.120.69 ± 0.10344lipid metabolic process; vesicle-mediated transport
21.00611.70.83 ± 0.150.50 ± 0.161.10 ± 0.150.64 ± 0.11435
    IPI00018783.1Inosine triphosphate pyrophosphatase (ITPA)11.00219.10.72 ± 0.130.58 ± 0.110.96 ± 0.240.76 ± 0.0952nucleotide metabolic process
21.00219.11.09 ± 0.380.77 ± 0.180.98 ± 0.150.64 ± 0.1152
    IPI00021700.3Proliferating cell nuclear antigen (PCNA)11.00838.30.74 ± 0.090.62 ± 0.080.68 ± 0.080.57 ± 0.08547DNA replication
21.001346.00.77 ± 0.120.59 ± 0.100.73 ± 0.120.56 ± 0.09556
    IPI00022977.1Creatine kinase B-type (CKB)11.00634.90.90 ± 0.170.57 ± 0.100.54 ± 0.140.35 ± 0.11204creatine metabolic process
21.001035.20.96 ± 0.260.68 ± 0.260.79 ± 0.360.61 ± 0.43175
    IPI00031420.3UDP-glucose 6-dehydrogenase (UGDH)11.00410.10.80 ± 0.130.66 ± 0.120.74 ± 0.110.61 ± 0.1094UDP-glucose metabolic process
21.00613.20.84 ± 0.110.70 ± 0.080.83 ± 0.090.70 ± 0.12135
    IPI00032313.1Protein S100-A4 (S100A4)11.00218.81.11 ± 0.131.25 ± 0.110.23 ± 0.050.25 ± 0.04192epithelial to mesenchymal transition
21.00318.81.09 ± 0.111.12 ± 0.160.32 ± 0.090.33 ± 0.10172
    IPI00033130.3SUMO-activating enzyme subunit 1 (SAE1)11.00312.70.75 ± 0.110.68 ± 0.210.76 ± 0.280.64 ± 0.1253Ubl conjugation pathway
21.0026.10.82 ± 0.170.67 ± 0.050.78 ± 0.160.65 ± 0.0951
    IPI00034319.2Isoform A of Protein CutA precursor (CUTA)11.00214.10.78 ± 0.150.69 ± 0.130.76 ± 0.130.68 ± 0.12152protein localization; response to metal ion
21.00214.10.73 ± 0.130.64 ± 0.110.72 ± 0.120.63 ± 0.11182
    IPI00220107.1Isoform 1 of Transcriptional regulator ATRX (ATRX)11.0021.70.70 ± 0.180.87 ± 0.310.64 ± 0.130.79 ± 0.2521DNA methylation
21.0021.10.78 ± 0.240.77 ± 0.250.80 ± 0.230.78 ± 0.1642
    IPI00293434.2Signal recognition particle 14 kDa protein (SRP14)11.00458.10.75 ± 0.080.70 ± 0.090.84 ± 0.170.77 ± 0.10133SRP-dependent cotranslational protein targeting to membrane
21.00319.90.86 ± 0.130.76 ± 0.070.86 ± 0.080.76 ± 0.09114
    IPI00375631.6Interferon-induced 17 kDa protein precursor (ISG15)11.00655.80.69 ± 0.131.06 ± 0.120.63 ± 0.120.97 ± 0.13395ISG15-protein conjugation
21.00738.80.67 ± 0.070.87 ± 0.120.62 ± 0.060.80 ± 0.09453
    IPI00449049.5Poly [ADP-ribose] polymerase 1 (PARP1)11.00813.70.96 ± 0.200.63 ± 0.130.98 ± 0.150.65 ± 0.14297DNA repair
21.00812.40.94 ± 0.200.64 ± 0.100.89 ± 0.170.61 ± 0.12266
    IPI00644020.1Sterol O-acyltransferase (Acyl-Coenzyme A: cholesterol acyltransferase) 1 (SOAT1)11.00316.50.87 ± 0.230.70 ± 0.030.66 ± 0.140.54 ± 0.0342cholesterol metabolic process
21.00211.50.72 ± 0.210.70 ± 0.240.69 ± 0.250.65 ± 0.1822
    IPI00646304.4Peptidylprolyl isomerase B precursor (PPIB)11.00942.60.66 ± 0.120.70 ± 0.110.81 ± 0.120.87 ± 0.08839protein folding
21.00943.50.67 ± 0.110.69 ± 0.100.82 ± 0.110.84 ± 0.11547
  • a Protein probability obtained from the ProteinProphet software.

  • b Mean, a weighted average of the peptide ratios per protein; S.D., standard deviation calculated among the peptide ratios per protein.

  • c C15 and C15-3, two independent mock clones; K3–8 and K3–14, two independent PRA1-knockdown stable clones.

  • d Functional classification of the dyesregulated proteins as revealed by annotation in the GO biological process categories.