Table I

The relative quantification of protein levels and mRNA levels in FDCP-Mix cells and TEL/PDGFRβ-FDCP-Mix cells

For comparison, 100 proteins (randomly selected proteins plus those in which changes between the two cell lines were seen using the isobaric tag quantification approach) were selected. Random selection was made via search databases (generating the accession codes shown: emb, EMBL; gb, GenBank™; pir, Protein Information Resource; rf, RefSeq (NCBI); spt, Swiss-Prot; trm, TrEMBL.). The total peptides columns refers to the number of peptides from that protein fragmented within three replicate experiments. The relative ratios for each protein were calculated as a weighted value combining averages from three replicate experiments. Ratios shown are: average control/control, an internal control, in which the same amount of the same lysate has been compared (ratio of 116:114, see Fig. 2b); average (1) oncogene/control, the ratio of protein in the TEL/PDGFRβ-transfected cells vs. control FDCP-Mix cells containing data from comparison of 117:114 iTRAQ label relative quantities; average (2) oncogene/control, containing data from comparison of 117:116 ratios. Also shown is the fold change in the mRNA level (-fold cDNA) for that transcript/protein (oncogene/control) according to microarray analysis. Sequences whose expression is significantly altered (p < 0.05) at the mRNA level are shown in italics.

AccessionProteinTotal peptidesAverage control/controlaAverage (1) oncogene/controlaAverage (2) oncogene/controla-Fold cDNA
pir|S3197514-3-3 protein ϵ71.1151.0610.9811.034
rf|NP_853613.114-3-3 protein γ81.0931.0721.0061.042
spt|P6310114-3-3 protein ζ81.1111.0430.9681.106
spt|P4791160S ribosomal protein L6101.0590.7850.7450.995
rf|NP_031501.1Acidic ribosomal phosphoprotein P071.0650.7890.7591.028
spt|P51881ADP, ATP carrier protein, fibroblast isoform181.1080.9990.9190.940
spt|Q60604Adseverin361.0661.0000.9741.040
spt|P47738Aldehyde dehydrogenase, mitochondrial51.0591.0741.0340.926
spt|P56480ATP synthase β chain, mitochondrial101.1231.2381.1271.058
Emb|CAA27396.1β-Actin641.1231.0610.9560.988
spt|Q9CWJ9Bifunctional purine biosynthesis protein71.0791.6911.661
Emb|CAA05361.1Bip131.1380.9760.8850.835
gb|AAA62450.1Calnexin151.0121.0101.0210.984
Spt|P14211Calreticulin (CRP55)411.1090.9390.8670.963
Spt|P97742Carnitine O-palmitoyltransferase41.1671.0240.9151.199
pir|HHMS60Chaperonin groEL130.8921.5381.7570.913
rf|NP_031662.1Chaperonin subunit 2 (β)91.0320.7460.7491.078
spt|P18760Cofilin, non-muscle isoform51.0811.0771.0151.008
prf|1513495ACu/Zn superoxide dismutase101.1101.0560.9730.996
rf|NP_031834.1Cytochrome c, somatic91.0880.8870.8290.885
spt|P49717DNA replication licensing factor MCM451.0750.8780.8271.234
Trm|Q8BMR3Dolichyl-diphosphooligosaccharide61.1260.9170.8211.085
sp|O70251Elongation factor 1-β41.0380.9520.9350.957
spt|P10126Elongation factor 1-α1641.0790.7970.7541.080
spt|P08113Endoplasmin precursor (GRP94)170.9991.1061.1760.876
rf|NP_075608.1Enolase 1, α non-neuron281.0931.1591.0731.036
rf|NP_031933.1Eukaryotic translation elongation factor 2271.1170.7710.7050.977
spt|P26040Ezrin121.0810.9690.9170.976
Trm|Q9EQR0Fatty acid synthase (Fasn protein)61.0220.8210.8241.003
spt|P35550Fibrillarin (Nucleolar protein 1)81.0500.9330.9001.030
rf|XP_127565.4Filamin B, β221.0520.8620.836
rf|XP_207130.3Filamin, α101.0020.9080.953
spt|P05064Fructose-bisphosphate aldolase A281.0541.2601.2241.041
rf|NP_032181.1Glucose phosphate isomerase 1131.0521.0371.0181.033
spt|P26443Glutamate dehydrogenase, mitochondrial71.1141.0550.9880.986
rf|NP_032110.1Glyceraldehyde-3-phosphate dehydrogenase291.0601.1261.0870.987
spt|P04187Granzyme B(G,H)261.1111.1941.1180.987
rf|NP_034566.1H2A histone family, member X271.0890.8170.7671.189
pir|JQ1983H3.3 like histone MH92181.0660.7990.7580.997
rf|NP_034610.1Heat-shock protein 1α361.0510.8350.8100.948
Emb|CAA56631.1High mobility group protein161.0541.1461.1071.040
rf|NP_085112.1Histone 1, H1a281.0291.2431.2670.880
rf|NP_056601.1Histone 1, H1c191.1120.9490.8750.827
rf|NP_835503.1Histone 1, h2bg321.0621.2611.2171.009
pir|S45110Histone H2A451.1420.8460.7621.138
gb|AAH58529.1Histone H4301.1110.9280.8561.095
spt|Q99020hnRNP A/B81.0491.1231.0970.985
gb|AAH06694.1hnRNP K protein111.1791.0770.9271.129
rf|NP_034829.1Lactate dehydrogenase 1, A chain361.1241.0400.9411.021
pir|JN0066Leukotriene-A4 hydrolase81.0730.8680.8270.878
emb|CAA65761.1M2-type pyruvate kinase511.1041.1371.0551.071
gb|AAA39509.1Malate dehydrogenase91.0361.0000.9780.945
rf|NP_620084.1Methylenetetrahydrofolate dehydrogenase 151.0450.9540.9321.022
rf|NP_034963.1Moesin141.0800.9750.9230.809
trm|Q9EQK1NADP+-specific isocitrate dehydrogenase111.1360.9300.8510.838
trm|Q8VDD5Nonmuscle heavy chain myosin II-A241.0631.0040.9571.069
sp|P09405Nucleolin (protein C23)171.0930.8920.8290.968
trm|Q8VDW0Nuclear RNA helicase, DECD variant of DEAD box family131.0881.0851.0210.918
rf|NP_077155.1Nucleolar protein 5A41.0531.2481.2220.952
spt|Q61937Nucleophosmin131.0990.7990.8050.905
pir|A46557Nucleoside-diphosphate kinase91.1030.9620.8950.963
spt|Q01768Nucleoside diphosphate kinase B71.1290.9060.8300.920
spt|P24369Peptidyl-prolyl cis-trans isomerase B61.1101.3301.1991.015
rf|NP_032933.1Peptidylprolyl isomerase A101.1191.1141.0021.051
spt|Q99K85Phosphoserine aminotransferase51.0511.1171.1131.103
rf|NP_035202.1Profilin 191.0551.0461.0041.114
spt|P27773Protein disulfide isomerase A3110.9840.9540.9860.931
rf|NP_033417.1RAN, member RAS oncogene family141.0671.2161.1800.983
spt|Q61599Rho GDP-dissociation inhibitor 241.1101.0260.9410.879
rf|NP_038749.1Ribosomal protein L7a81.0050.9370.9251.072
rf|NP_079862.1Ribosomal protein L1580.9510.8620.9211.083
rf|NP_075029.1Ribosomal protein L23181.1190.9280.8590.998
rf|NP_035430.1Ribosomal protein S761.1050.9290.8491.052
rf|NP_084043.1Ribosomal protein S9-like71.1230.9290.8491.003
rf|NP_080809.1Ribosomal protein S1391.1200.9030.8280.987
gb|AAA16796.1Ribosomal protein S1871.0700.8010.7631.092
trm|Q7TNQ6Ribosomal protein, large P261.0710.7090.6841.015
spt|Q08943Structure-specific recognition protein 161.1101.1040.9211.086
rf|NP_063932.1Succinate-CoA ligase, GDP-forming, α71.0711.1171.0660.901
gb|AAA40338.1T complex polypeptide 170.9720.9050.9701.219
spt|P26039Talin 1120.9761.0760.9861.029
spt|Q9WVA4Transgelin 2101.0471.0060.9821.089
spt|P40142Transketolase161.0740.8350.7900.922
pir|JL0149Transplantation antigen P19851.0430.8390.8161.089
pir|ISMSTTriosephosphate isomerase111.0551.3101.2841.160
rf|NP_666228.1Tubulin, β, 2541.1090.6420.6021.081
gb|AAH43053.1Valosin containing protein151.0681.0190.9810.985
Differentially expressed proteins as determined by iTRAQ
    spt|Q6443310-kDa heat shock protein51.0791.513***1.402***0.989
    spt|P4563460S ribosomal protein L10121.0720.624*0.593*1.013
    gb|AAH21937.1Aldo-keto reductase family 1, C13221.1050.770*0.798*1.072
    spt|P28293 Cathepsin G 9 1.059 0.617 *** 0.621 *** 0.532
    pir|A45935DnaK-type molecular chaperone hsc70371.0570.813**0.794***0.892
    rf|NP_853613.1Eukaryotic translation initiation factor 5A121.1370.498***0.448***0.961
    gb|AAA37866.184-kDa heat-shock protein341.0870.712***0.668***0.955
    rf|NP_031542.1Heterogeneous nuclear ribonucleoprotein D71.0681.382**1.337*0.996
    spt|Q61233 l -plastin 40 1.081 0.748* 0.702** 0.745
    spt|P43430 Mast cell protease 8 3 1.062 0.318* 0.312** 0.352
    Trm|Q7TMS4 Myeloperoxidase protein 10 1.035 0.307 *** 0.302 *** 0.219
    Spt|P09103 Protein disulfide isomerase 27 1.122 0.696 *** 0.631 *** 0.763
    spt|Q60931Voltage-de pend ent anion-selective channel protein 351.0580.638**0.629**1.146
  • a Statistical significance of the change as determined by Student t test is depicted (

  • * , p < 0.05;

  • ** , p < 0.01;

  • *** , p < 0.001).