Table II

Proteins identified to be significantly (p < 0.05) affected by IR in the wild type thymocyte samples

NCBI accession no.DescriptionGene symbolRatio (−IR/+IR)S.D.Pepa
NP_001005331 Eukaryotic translation initiation factor 4, γ1 Eif4g1 0.050.011
NP_598445 MOCO sulfurase C-terminal domain-containing 2 Mosc2 0.050.012
NP_080750 SGT1, suppressor of G2 allele of SKP1 Sugt1 0.050.012
NP_067498 HECT, UBA, and WWE domain-containing 1 Huwe1 0.100.011
NP_001074525 Exportin, tRNA Xpot 0.100.012
NP_038946 Ubiquitin-specific peptidase 25 Usp25 0.110.021
NP_598924 Muscleblind-like 3 Mbnl3 0.120.021
NP_033140 S100 calcium-binding protein A9 (calgranulin B) S100a9 0.130.046
NP_035831 Vimentin Vim 0.140.033
NP_038678 S100 calcium-binding protein A8 (calgranulin A) S100a8 0.140.024
NP_033980 CD3 antigen, γ polypeptide Cd3g 0.160.031
NP_663521 General transcription factor IIB Gtf2b 0.170.022
NP_034692 Integrin-linked kinase Ilk 0.180.011
NP_113581 Actin-like 6B Actl6b 0.180.032
NP_080858 Putative NF-κ B-activating protein 373 Gpr177 0.190.032
NP_032548 Lactotransferrin Ltf 0.190.1211
NP_032246 Hemoglobin, β adult major chain Hbb-b1 0.190.036
NP_058063 Progesterone receptor membrane component Pgrmc1 0.210.012
NP_062414, NP_034114Cathepsin 8, cathepsin L preproproteinCts8, Ctsl0.210.023
NP_034022 Chitinase 3-like 3 Chi3l3 0.210.138
NP_064432 Trf-proximal protein homolog Trfp 0.220.031
NP_031960 Glutamyl aminopeptidase Enpep 0.220.031
NP_001074599 Oxoglutarate dehydrogenase-like Ogdhl 0.220.022
NP_033784 Albumin 1 Alb 0.230.1319
NP_059066 Haptoglobin Hp 0.230.041
NP_067448 Aldo-keto reductase family 1, member A4 (aldehyde reductase) Akr1a4 0.240.062
NP_032199 Nuclear receptor subfamily 3, group C, member 1 Nr3c1 0.250.042
NP_031650 Chromobox homolog 3 Cbx3 0.250.062
NP_038499 Annexin A4 Anxa4 0.260.025
NP_937812 Glucocorticoid modulatory element-binding protein 2 Gmeb2 0.260.022
NP_062513, NP_075679Apoptotic chromatin condensation inducer 1 Acin1 0.260.012
NP_032255 Histone deacetylase 2 Hdac2 0.270.042
NP_067620 Nicastrin Ncstn 0.270.021
NP_035908 Coronin, actin-binding protein 1B Coro1b 0.270.062
NP_033941 Caspase 6 Casp6 0.280.083
NP_082568 Protein phosphatase methylesterase 1 Ppme1 0.280.032
NP_038853 Lymphocyte antigen 75 Ly75 0.280.064
NP_996988 Response to metastatic cancers 1 H2-Ab1 0.280.1012
NP_058020 S100 calcium-binding protein A11 (calizzarin) S100a11 0.280.035
NP_444389 Mitochondrial ribosomal protein L3 Mrpl3 0.290.051
NP_032720 Neutrophilic granule protein Ngp 0.290.064
NP_031652 Chromobox homolog 5 (DrosophilaHP1a) Cbx5 0.300.094
NP_036153, NP_036154, NP_033384, NP_937811Regulatory subunit B56, protein phosphatase 2Ab0.300.042
NP_780519 Androgen-induced proliferation inhibitor Pds5b 0.300.064
NP_034764 Fatty acid-binding protein 5 Fabp5 0.300.054
NP_062708 N-Acylsphingosine amidohydrolase (acid ceramidase) 1 Asah1 0.310.032
NP_034954 Myeloperoxidase Mpo 0.320.057
XP_194337 Multiple EGF-like domains 8 Megf8 0.320.051
NP_035753 Topoisomerase (DNA) II α Top2a 0.330.043
NP_444354 SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 5 Smarca5 0.330.052
NP_034623 Intercellular adhesion molecule Icam1 0.330.042
NP_056594 Neutrophil elastase Ela2 0.330.022
NP_035840 Tryptophanyl-tRNA synthetase Wars 0.340.044
NP_081212 Oxidase assembly 1-like Oxa1l 0.340.031
NP_062709 APAF1-interacting protein Apip 0.340.022
NP_033364 Acetyl-coenzyme A acetyltransferase 2 Acat2 0.340.072
NP_034960 MutS homolog 6 Msh6 0.350.043
NP_036151 Peroxiredoxin 5 precursor Prdx5 0.350.072
NP_064337 Transmembrane protein 4 Tmem4 0.360.074
NP_892035 Structure-specific recognition protein 1 Ssrp1 0.370.042
NP_058622 Squamous cell carcinoma antigen recognized by T-cells 3 Sart3 0.370.041
NP_766283 Phospholipase A2, activating protein Plaa 0.370.052
NP_033357 Transcription factor 7, T-cell-specific Tcf7 0.380.052
NP_038579 Hydroxymethylbilane synthase Hmbs 0.380.061
NP_598738 Transferrin Trf 0.390.062
NP_080070 Electron transferring flavoprotein dehydrogenase Etfdh 0.400.083
NP_775621 RCC1 domain-containing 1 Rccd1 0.400.031
NP_036167 Vesicle amine transport protein 1 homolog (Torpedo californica) Vat1 0.410.043
NP_082442 Hypothetical protein LOC72244 1600014C10Rik 0.410.163
NP_034851 Lamin B1 Lmnb1 0.450.193
NP_034793 Keratin complex 1, acidic, gene 17 Krt17 0.450.133
NP_080784 TNF receptor-associated protein 1 Trap1 1.490.012
NP_067497 Ubiquitin-specific protease 14 Usp14 1.780.022
NP_114084 SWI/SNF related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 2 Smarcd2 1.870.063
NP_035407 Ring finger protein 2 Rnf2 2.390.241
NP_080120 Cysteine- and histidine-rich domain (CHORD)-containing, zinc-binding protein 1 Chordc1 2.590.323
NP_077180 Ribosomal protein L24 Rpl24 2.600.507
NP_033035 RAD21 homolog Rad21 2.640.295
NP_034745 Kinesin family member 11 Kif11 2.690.092
NP_036105 Ribosomal protein L27a Rpl27a 2.700.532
NP_683747,NP_080225, NP_033123,NP_035429Ribosomal protein S6 kinasec2.970.642
NP_666054 3-Hydroxy-3-methylglutaryl-coenzyme A synthase 1 Hmgcs1 3.050.392
NP_150289 Cyclic AMP-regulated phosphoprotein, 21 isoform 2 Arpp21 3.080.421
NP_038484 Actinin α 3 Actn3 3.120.512
NP_766607 6-Phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 Pfkfb4 3.290.482
NP_033785 Activated leukocyte cell adhesion molecule Alcam 3.370.522
NP_081626 Asparaginyl-tRNA synthetase Nars 3.460.351
NP_033109 Ribosomal protein L30 Rpl30 3.520.444
NP_033120 Ribosomal protein S4, X-linked Rps4x 3.960.708
NP_033240 Spermine synthase Sms 3.960.442
NP_062648 Protein phosphatase 4, catalytic subunit Ppp4c 4.070.681
NP_796307 SEC6-like 1 Exoc3 4.170.651
NP_082253 RIKEN cDNA 2310001A20 2310001A20Rik 4.640.453
NP_780314 Aquaporin 11 Aqp11 5.780.681
NP_038573 Hemopoietic cell phosphatase Ptpn6 6.552.004
NP_081291 Ribosomal protein S27 Rps27 7.261.482
NP_569054 Toll-like receptor 3 Tlr3 8.912.642
NP_075029 Ribosomal protein L23 Rpl23 9.761.822
NP_112442 Heat shock protein 8 Hspa8 14.423.272
  • a For proteins identified by a single peptide, the sequence, precursor mass, charge, and Xcorr score for the peptide identified is provided in supplemental Table 2; MS/MS spectra for those peptides are provided in supplemental Fig. 3.

  • b Unable to discriminate the γ, ε, δ, and β isoforms.

  • c Unable to discriminate polypeptides 1, 2, 3, and 6.