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Table 2 Top-hit list of differentially expressed proteins in CD4+ T cells

From: Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls

Accession Protein identity Gene names p-value FC MS versus HC (log2) Median intensity MS (log2) MS SD Median intensity HC (log2) HC SD % seq cov # pep AUC
Q5JSL3 Dedicator of cytokinesis protein 11 DOCK11 4.69E−05 0.27405 22.73205 0.14968 22.458 0.11384 13 21 0.98
Q03252 Lamin-B2 LMNB2 0.000203 0.2023 26.23395 0.10367 26.03165 0.1219 58.1 42 0.94
Q14978 Nucleolar and coiled-body phosphoprotein 1 NOLC1 0.000306 0.67815 21.4053 0.26237 20.72715 0.36787 16.2 9 0.92
Q2M2I8; Q9NSY1 AP2-associated protein kinase 1 AAK1 0.000457 0.22605 23.1178 0.11404 22.89175 0.12897 33 20 0.92
Q13148 TAR DNA-binding protein 43 TARDBP 0.000642 0.29 23.3943 0.12816 23.1043 0.14754 39.4 11 0.89
P20963 T-cell surface glycoprotein CD3 zeta chain CD247 0.000907 0.19535 23.48275 0.0965 23.2874 0.18125 60.4 11 0.88
P49959 Double-strand break repair protein MRE11A MRE11A 0.001405 0.1957 21.44665 0.17074 21.25095 0.15881 21.6 11 0.88
P06239 Tyrosine-protein kinase Lck LCK 0.001598 0.2009 24.642 0.12459 24.4411 0.13158 49.7 18 0.85
Q9NR56; Q5VZF2; Q9NUK0 Muscleblind-like protein 1 MBNL1 0.001651 0.3464 22.0867 0.19817 21.7403 0.24361 21.6 8 0.87
P35573 Glycogen debranching enzyme; 4-alpha-glucanotransferase; amylo-alpha-1,6-glucosidase AGL 0.00177 0.32245 21.79335 0.29915 21.4709 0.18837 18.1 18 0.87
P18085 ADP-ribosylation factor 4 ARF4 0.00199 − 0.29765 21.6712 0.17375 21.96885 0.14457 64.4 10 0.86
O75131; Q96FN4; Q8IYJ1; Q9HCH3; Q9UBL6 Copine-3 CPNE3 0.002255 0.1118 23.9288 0.09682 23.817 0.07363 46.7 19 0.88
P27824 Calnexin CANX 0.002331 − 0.2029 24.6288 0.09381 24.8317 0.13864 37.7 22 0.85
Q49A26 Putative oxidoreductase GLYR1 GLYR1 0.002442 0.2299 22.8002 0.15088 22.5703 0.13549 40 14 0.88
P12694 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial BCKDHA 0.002513 0.2997 20.58005 0.14155 20.28035 0.16289 21.1 6 0.89
P16615 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 ATP2A2 0.002577 − 0.34015 20.91155 0.24663 21.2517 0.39528 22.5 15 0.85
P31146; REV__Q02818 Coronin-1A CORO1A 0.002667 0.196 28.77805 0.04311 28.58205 0.14531 63.8 33 0.91
P29401 Transketolase TKT 0.002709 0.18195 27.0961 0.16375 26.91415 0.08497 68.9 38 0.86
Q00610; P53675 Clathrin heavy chain 1 CLTC 0.00312 − 0.10695 26.3723 0.05858 26.47925 0.08019 58.7 80 0.83
P19971 Thymidine phosphorylase TYMP 0.003318 − 0.6095 21.51775 0.63532 22.12725 0.52772 51 16 0.85
Q16401 26S proteasome non-ATPase regulatory subunit 5 PSMD5 0.003478 0.12765 23.7053 0.09891 23.57765 0.13094 58.9 21 0.86
Q15084 Protein disulfide-isomerase A6 PDIA6 0.003546 − 0.3043 23.5948 0.25739 23.8991 0.17192 45.9 13 0.86
P07237 Protein disulfide-isomerase P4HB 0.003888 − 0.1857 25.1359 0.14266 25.3216 0.09151 56.1 27 0.85
O43665 Regulator of G-protein signaling 10 RGS10 0.003925 0.2594 23.5918 0.213 23.3324 0.14464 60.1 12 0.85
P27986; O00459 Phosphatidylinositol 3-kinase regulatory subunit alpha PIK3R1 0.004008 0.2604 22.56095 0.17873 22.30055 0.21783 38.3 19 0.83
Q9Y4L1 Hypoxia up-regulated protein 1 HYOU1 0.004021 − 0.1815 23.00205 0.13058 23.18355 0.13156 31.8 20 0.83
O75306 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial NDUFS2 0.004057 0.13545 22.6738 0.08259 22.53835 0.13156 34.8 12 0.83
Q8WUX9 Charged multivesicular body protein 7 CHMP7 0.004115 0.23275 21.9775 0.21092 21.74475 0.18291 37.1 13 0.81
P07602 Prosaposin; Saposin-A; Saposin-B-Val; Saposin-B; Saposin-C; Saposin-D PSAP 0.004366 − 0.19325 22.296 0.18336 22.48925 0.42157 12.6 6 0.94
O00422 Histone deacetylase complex subunit SAP18 SAP18 0.004452 0.37715 20.6193 0.18761 20.24215 0.34985 41.8 5 0.87
Q9ULA0 Aspartyl aminopeptidase DNPEP 0.004664 0.3613 23.6397 0.17228 23.2784 0.18788 53.3 18 0.82
O43681 ATPase ASNA1 ASNA1 0.004954 − 0.11665 22.25215 0.13672 22.3688 0.11129 50.6 10 0.83
O75832 26S proteasome non-ATPase regulatory subunit 10 PSMD10 0.004963 0.21305 21.312 0.24569 21.09895 0.12837 40.3 6 0.89
P30536 Translocator protein TSPO 0.004964 0.5376 22.44845 0.37985 21.91085 0.337 23.1 3 0.82
P24666 Low molecular weight phosphotyrosine protein phosphatase ACP1 0.005013 0.2241 22.8028 0.19373 22.5787 0.20543 72.2 8 0.88
Q4G176 Acyl-CoA synthetase family member 3, mitochondrial ACSF3 0.005127 0.3234 20.8339 0.32659 20.5105 0.20115 19.3 7 0.83
P35611 Alpha-adducin ADD1 0.005201 0.17245 23.941 0.12213 23.76855 0.20616 44.9 24 0.81
P19525 Interferon-induced, double-stranded RNA-activated protein kinase EIF2AK2 0.005211 − 0.54585 20.65625 0.47474 21.2021 0.40633 20.1 9 0.87
O75791 GRB2-related adapter protein 2 GRAP2 0.00589 0.1927 23.58335 0.07421 23.39065 0.15601 43 13 0.84
Q16666; Q6N021 Gamma-interferon-inducible protein 16 IFI16 0.006051 − 0.27745 24.51685 0.24674 24.7943 0.12775 43.4 31 0.84
Q9HAV4 Exportin-5 XPO5 0.006457 − 0.402 18.4781 0.23884 18.8801 0.22546 5.1 4 0.87
Q9NRY5 Protein FAM114A2 FAM114A2 0.006779 0.4935 19.3331 0.23485 18.8396 0.34369 15.8 4 0.86
P11177 Pyruvate dehydrogenase E1 component subunit beta, mitochondrial PDHB 0.006838 0.2322 24.05355 0.11379 23.82135 0.12468 52.9 13 0.83
Q9NZZ3 Charged multivesicular body protein 5 CHMP5 0.006962 − 0.28845 20.37145 0.31795 20.6599 0.20311 40.6 6 0.83
P53634 Dipeptidyl peptidase 1; dipeptidyl peptidase 1 exclusion domain chain; dipeptidyl peptidase 1 heavy chain; dipeptidyl peptidase 1 light chain CTSC 0.006992 − 0.36305 20.5409 0.54754 20.90395 0.10359 19.9 7 0.81
Q06546 GA-binding protein alpha chain GABPA 0.006996 0.2074 21.3763 0.1983 21.1689 0.20734 28 8 0.8
P21399 Cytoplasmic aconitate hydratase ACO1 0.008051 0.1699 21.4757 0.14153 21.3058 0.20875 20.4 11 0.82
Q9H400 Lck-interacting transmembrane adapter 1 LIME1 0.008125 0.25515 21.11 0.19997 20.85485 0.21307 46.1 7 0.81
Q02750 Dual specificity mitogen-activated protein kinase kinase 1 MAP2K1 0.00822 0.1771 23.2231 0.13291 23.046 0.1348 42.2 14 0.8
O94826 Mitochondrial import receptor subunit TOM70 TOMM70A 0.008231 0.21725 22.34995 0.15186 22.1327 0.20502 34.5 13 0.81
O75475 PC4 and SFRS1-interacting protein PSIP1 0.008443 0.1899 22.08185 0.1504 21.9335 0.15516 45.5 21 0.8
P02776 Platelet factor 4; platelet factor 4, short form PF4 0.008535 − 1.5035 24.86845 1.22842 24.67855 1.48716 36.6 5 0.83
Q5XKP0 Protein QIL1 QIL1 0.008552 0.31595 22.7718 0.27181 24.2753 0.34286 62.7 3 0.84
Q9UGI8 Testin TES 0.008688 0.14215 19.94335 0.09764 19.6274 0.12853 72 31 0.8
Q86VP6; O75155 Cullin-associated NEDD8-dissociated protein 1 CAND1 0.008724 0.11355 25.3342 0.10321 25.19205 0.08176 48.9 46 0.84
Q9C0K0 B-cell lymphoma/leukemia 11B BCL11B 0.008892 0.2434 25.65085 0.17505 25.5373 0.22495 12.8 8 0.79
P13861; P31323 cAMP-dependent protein kinase type II-alpha regulatory subunit PRKAR2A 0.008993 0.13145 21.90015 0.12538 21.65675 0.09173 62.1 20 0.81
P07741 Adenine phosphoribosyltransferase APRT 0.008995 0.19165 23.14455 0.1699 23.0131 0.15824 91.1 17 0.83
P23246 Splicing factor, proline- and glutamine-rich SFPQ 0.009648 0.12175 25.8719 0.14919 25.68025 0.09657 47.9 31 0.83
P49903 Selenide, water dikinase 1 SEPHS1 0.009747 0.2257 26.39505 0.15139 26.2733 0.15099 41.6 10 0.83
P62995 Transformer-2 protein homolog beta TRA2B 0.009757 0.17515 22.6718 0.18232 22.4461 0.12504 30.9 8 0.8
Q86XP3 ATP-dependent RNA helicase DDX42 DDX42 0.009985 0.1467 23.91205 0.20211 23.7369 0.12402 22.7 13 0.85
P13010 X-ray repair cross-complementing protein 5 XRCC5 0.01116 0.2196 22.23445 0.1468 22.08775 0.12306 71.2 48 0.82
Q15428 Splicing factor 3A subunit 2 SF3A2 0.011498 0.30175 25.0703 0.2546 25.26055 0.28193 28.7 9 0.85
P37837 Transaldolase TALDO1 0.011683 0.26525 24.0953 0.16309 23.9199 0.1934 47.2 19 0.8
O94973 AAK1 AP2A2 0.01208 0.40715 22.87215 0.18724 22.7054 0.31295 25 16 0.82
P16150 Leukosialin SPN 0.012636 0.41995 27.0869 0.31488 26.8673 0.23838 19.5 5 0.8
Q9Y6K5 2-5-oligoadenylate synthase 3 OAS3 0.013062 − 0.58225 24.1071 0.61142 23.9796 0.40043 26.2 21 0.8
P13598 Intercellular adhesion molecule 2 ICAM2 0.013215 − 0.33575 22.4839 0.36073 22.18215 0.13532 14.9 3 0.81
O96000 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 NDUFB10 0.013266 0.2682 27.0077 0.2602 26.74245 0.17232 43 7 0.82
P48059; Q7Z4I7 LIM and senescent cell antigen-like-containing domain protein 1 LIMS1 0.013613 − 1.11835 22.2423 1.06748 22.4974 1.04857 45.8 13 0.83
P0DOX5; P01857 Ig gamma-1 chain C region IGHG1 0.014981 − 0.8553 21.9197 0.96324 21.51255 0.41275 28.3 9 0.8
P67936 Tropomyosin alpha-4 chain TPM4 0.015875 − 0.39585 22.849 0.50209 22.42905 0.33951 66.1 27 0.81
Q53QZ3 Rho GTPase-activating protein 15 ARHGAP15 0.016084 0.2283 22.7616 0.11442 22.6226 0.26067 28.8 10 0.8
Q93077; Q7L7L0; P04908 Histone H2A type 1-C; histone H2A type 3; histone H2A type 1-B/E HIST1H2AC; HIST3H2A; HIST1H2AB 0.016472 0.5318 24.6077 0.68101 24.4913 0.51829 35.4 7 0.83
Q00341 Vigilin HDLBP 0.017653 − 0.3557 22.1316 0.25975 22.71385 0.26847 5.3 5 0.8
Q9Y3C4 EKC/KEOPS complex subunit TPRKB TPRKB 0.01784 0.33545 25.2378 0.31196 25.04925 0.2556 56.6 7 0.83
Q96I24 Far upstream element-binding protein 3 FUBP3 0.018912 0.2288 19.18425 0.18212 19.52 0.15408 24.7 9 0.81
P18206 Vinculin VCL 0.019685 − 0.57615 22.07985 0.84436 21.81165 0.52692 64.2 60 0.83
Q96BW5 Phosphotriesterase-related protein PTER 0.020487 0.35515 23.0556 0.21492 22.8575 0.29673 24.4 6 0.82
P02775 Platelet basic protein; connective tissue-activating peptide III; TC-2; connective tissue-activating peptide III(1-81); beta-thromboglobulin; neutrophil-activating peptide 2(74); neutrophil-activating peptide 2(73); neutrophil-activating peptide 2; TC-1; Neutrophil-activating peptide 2(1–66); neutrophil-activating peptide 2(1–63) PPBP 0.022319 − 1.4945 21.6995 1.19479 21.55895 1.23096 38.3 5 0.81
P21333 Filamin-A FLNA 0.023825 − 0.23365 21.21755 0.43258 22.3359 0.24022 71.6 137 0.81
Q01469; A8MUU1 Fatty acid-binding protein, epidermal FABP5 0.024356 − 0.5329 26.41625 0.73245 26.33375 0.55502 76.3 11 0.83
O94903 Proline synthase co-transcribed bacterial homolog protein PROSC 0.024792 0.27275 24.465 0.13221 24.3072 0.20226 37.8 8 0.8
P21291 Cysteine and glycine-rich protein 1 CSRP1 0.026425 − 0.2011 25.4829 0.36999 25.34655 0.16603 64.2 8 0.8
P53041 Serine/threonine-protein phosphatase 5 PPP5C 0.028586 0.2748 23.5436 0.14823 23.3623 0.29589 22.8 8 0.84
Q8WUM0 Nuclear pore complex protein Nup133 NUP133 0.030136 0.272 21.15755 0.26096 22.01285 0.19541 18.3 12 0.81
P09525 Annexin A4 ANXA4 0.032901 − 0.25805 26.25495 0.30546 26.6508 0.2431 47.6 13 0.82
Q04826 HLA class I histocompatibility antigen, B-40 alpha chain HLA-B 0.033546 − 1.0305 21.98915 0.72834 21.76085 0.84434 44.5 13 0.81
O43704 Sulfotransferase family cytosolic 1B member 1 SULT1B1 0.035541 0.4495 26.00495 0.2866 26.19745 0.42792 39.2 9 0.82
  1. The table displays proteins (n = 90) that are differentially expressed in CD4+ T cells from MS patients compared to healthy controls (HC). The proteins are extracted from Additional file 1: Table S1 and selected by fulfilling at least two of the three criteria: p-value (p < 0.01), area under the curve (AUC) (AUC > 0.8) and log fold-change (FC) > [0.2] between samples from MS patients and healthy controls. The log2-fold changes in MS versus HC are based on normalized values. Accession number, protein identity and gene names are indicated for each protein, in addition to median log2-transformed protein abundances with standard variation (SD) for each group, the percentage of sequence coverage (% seq cov) and number of peptides (# pep) identified for each protein