Gene Expression Subtypes in Patients with Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (Table 2) Table 2. Characteristics of differentially expressed genes in chronic fatigue syndrome/myalgic encephalomyelitis. ------------------------------------------------------------------------------------------------------------------ Gene Gene name GenBank TaqMan assay Microarray Real-time PCR symbol accession identification no.a fold Fold 2-tailed P no. difference difference ------------------------------------------------------------------------------------------------------------------ ABCD4b ATP-binding cassette, subfamily D NM_020323 Hs00245340_m1 NA 2.08 .028 (ALD), member 4 ACTR3 ARP3 actin-related protein 3 NM_005721 Hs00828586_m1 4.55 1.42 .0042 homolog (yeast) AKAP10 A-kinase (PRKA) anchor protein 10 NM_007202 Hs00183673_m1 12.5 1.54 .0011 ANAPC11b APC11 anaphase promoting complex NM_016476 Hs00212858_m1 6.3 3.32 .00033 subunit 11 homolog (yeast) ANAPC5 Anaphase promoting complex NM_016237 Hs00212120_m1 8.25 2.36 .00016 subunit 5 APP Amyloid beta (A4) precursor protein NM_201413 Hs00169098_m1 3.1 2.5 4.33 10-9 ARL4C ADP-ribosylation factorlike 4C NM_005737 Hs00255039_s1 2.23 2.96 8.90 10-6 ARPC5 Actin-related protein 2/3 complex, NM_005717 Hs00271722_m1 4.8 3.23 6.82 10-8 subunit 5 ARSD Arylsulfatase D NM_001669 Hs00534692_m1 6.97 1.98 .001 ATP6V1C1 ATPase, H+ transporting, lysosomal NM_001695 Hs00184625_m1 3.8 2.03 .00029 V1 subunit C1, 42 kDa BCOR BCL6 corepressor NM_017745 Hs00372369_m1 2.95 1.6 .0098 BMP2K BMP2 inducible kinase NM_198892 Hs00214079_m1 1.67 1.3 .014 BRMS1b Breast cancer metastasis suppressor 1 NM_015399 Hs00363036_m1 4 2.68 .0014 CD2BP2 b CD2 (cytoplasmic tail) binding protein 2 NM_006110 Hs00272036_m1 3.6 1.8 5.35 10-6 CD47 CD47 molecule NM_198793 Hs00179953_m1 1.62 2.2 .00013 CEP350 Centrosomal protein, 350 kDa NM_014810 Hs00402774_m1 2.05 2.02 .0048 CITED2 Cbp/p300-interacting transactivator, NM_006079 Hs00366696_m1 7.05 2.39 4.45 10-6 with Glu/Asp-rich carboxy terminal domain, 2 CMTM6 CKLF-like MARVEL transmembrane NM_017801 Hs00215083_m1 1.6 1.41 .012 domain containing 6 CREBBP CREB binding protein (Rubinstein- NM_004380 Hs00231733_m1 2.37 1.43 .016 Taybi syndrome) CRK v-crk sarcoma virus CT10 oncogene NM_016823 Hs00180418_m1 2.2 2.51 1.11 10-5 homolog (avian) CTBP1 C-terminal binding protein 1 NM_001328 Hs00179922_m1 2.85 1.45 .062 CXCR4 C-terminal binding protein 1 NM_003467 Hs00607978_s1 2.7 1.67 7.80 10-5 EBI2 Epstein-Barr virus-induced gene NM_004951 Hs00270639_s1 1.3 3.44 .0012 2 (lymphocyte-specific GPCR) EIF2B4b Eukaryotic translation initiation factor NM_172195 Hs00248984_m1 2.06 .025 2B, subunit 4 delta, 67 kDa EIF3S10 Eukaryotic translation initiation factor NM_003750 Hs00186707_m1 1.7 3.58 .0029 3, subunit 10 thata, 150/170kDa EIF4G1b Eukaryotic translation initiation factor NM_198241 Hs00191933_m1 3.05 .0033 4A, isoform 2 EIF4G3 Eukaryotic translation initiation factor NM_003760 Hs00186804_m1 1.4 1.67 1.37 10-5 4 gamma, 3 FAM126B Family with sequence similarity 126, NM_173822 Hs00545158_m1 2.35 1.64 .0034 member B FNTA Farnesyltransferase, CAAX box, NM_002027 Hs00357739_m1 2.6 2.18 3.82 10-6 GABARAPL1b GABA(A) receptor associated NM_031412 Hs00744468_s1 1.65 5.64 6.10 10-5 protein-like 1 GCN1L1 GCN1 general control of amino acid NM_006836 Hs00412445_m1 2.45 2.05 .00052 synthesis 1-like 1 (yeast) GLTSCR2 Glioma tumor suppressor candidate NM_015710 Hs00414236_m1 3.7 1.24 .026 region gene 2 GNAS GNAS complex locus NM_080425 Hs00255603_m1 1.7 1.7 1.09 10-7 GSN b Gelsolin (amyloidosis, Finnish type) NM_198252 Hs00609276_m1 3.62 2.93 .00017 GTF2A2 General transcription factor IIA, 2, 12 NM_004492 Hs00362112_m1 1.25 1.79 .03 kDa HIF1A Hypoxia-inducible factor 1, alpha subunit NM_001530 Hs00153153_m1 0.6 0.81 .016 IFNAR1 Interferon (-alpha,-beta, and -omega) NM_000629 Hs00265057_m1 2.2 1.76 .00073 receptor 1 IL10RAb Interleukin-10 receptor, alpha NM_001558 Hs00387004_m1 1.7 1.73 9.87 10-6 IL6R Interleukin-6 receptor NM_000565 Hs00794121_m1 1.45 1.19 .06 IL6ST Interleukin-6 signal transducer NM_002184 Hs00174360_m1 2.12 1.8 .002 IL7R Interleukin-7 receptor NM_002185 Hs00233682_m1 0.45 0.82 .032 JAK1 Janus kinase 1 (a protein tyrosine NM_002227 Hs00233820_m1 1.85 1.91 1.86 10-8 kinase) KHSRP b KH-type splicing regulatory protein NM_003685 Hs00269352_m1 6.5 1.67 .00026 (FUSE binding protein 2) Table 2. Characteristics of differentially expressed genes in chronic fatigue syndrome/myalgic encephalomyelitis. ------------------------------------------------------------------------------------------------------------------ Gene Gene name GenBank TaqMan assay Microarray Real-time PCR symbol accession identification no.a fold Fold 2-tailed P no. difference difference ------------------------------------------------------------------------------------------------------------------ MAPK9 Mitogen-activated protein kinase 9 NM_139070 Hs00177102_m1 2.75 1.4 .045 METTL3 Methyltransferase-like 3 NM_019852 Hs00219820_m1 2.55 2.06 .0001 MRPL23 b Mitochondrial ribosomal protein L23 NM_021134 Hs00221699_m1 3.4 2.06 .001 MRPS6 Mitochondrial ribosomal protein S6 NM_032476 Hs00606808_m1 1.47 1.53 .025 MRRF Mitochondrial ribosome recycling NM_138777 Hs00751845_s1 4.6 8.91 .0004 factor MSNc Moesin NM_002444 Hs00792607_mH 2.1 1.33 .0016 MTMR6 Myotubularin-related protein 6 NM_004685 Hs00395064_m1 2.95 1.71 .0025 NFKB1 Nuclear factor of kappa light polypeptide NM_003998 Hs00231653_m1 2.8 1.59 4.04 10-5 gene enhancer in B-cells 1 (p105) NR1D2 Nuclear receptor subfamily 1, group NM_005126 Hs00233309_m1 2.1 2.44 .00076 D, member 2 NTE b Neuropathy target esterase NM_006702 Hs00198648_m1 3.5 1.7 .04 NUFIP2 Nuclear fragile X mental retardation NM_020772 Hs00325168_m1 5.6 1.5 .00036 protein interacting protein 2 PAPOLA Poly(A) polymerase alpha NM_032632 Hs00413685_m1 1.74 1.32 .00194 PDCD2 b Programmed cell death 2 NM_002598 Hs00751277_sH 2.55 6.76 .0096 PDCD6 Programmed cell death 6 NM_013232 Hs00737034_m1 2.6 1.74 .00019 PEX16 b Peroxisomal biogenesis factor 16 NM_004813 Hs00191337_m1 4.2 1.74 .0034 PGM2 Phosphoglucomutase 2 NM_018290 Hs00217619_m1 2.05 2.17 1.68 10-6 PIK3R1 Phosphoinositide-3-kinase, regulatory NM_181523 Hs00236128_m1 0.45 0.68 .025 subunit 1 (p85 alpha) PKN1b Protein kinase N1 NM_213560 Hs00177028_m1 1.7 1.56 9.40 10-5 POLR2G b Polymerase (RNA) II (DNA-directed) NM_002696 Hs00275738_m1 2.3 2.58 .0078 polypeptide G PPP2R5C Protein phosphatase 2, regulatory NM_002719 Hs00604902_m1 1.83 1.38 .022 subunit B (B56), gamma isoform PRKAA1 Protein kinase, AMP-activated, alpha 1 NM_006251 Hs01562315_m1 2.22 1.72 .00052 catalytic subunit PRKAR1A Protein kinase, cAMP-dependent, NM_002734 Hs00267597_m1 1.3 2.63 2.91 10-8 regulatory, type I, PUM2 Pumilio homolog 2 (Drosophila) NM_015317 Hs00209677_m1 2.7 1.39 .00064 RAP2C RAP2C, member of RAS oncogene NM_021183 Hs00221801_m1 1.85 2.1 .015 family RNF141 Ring finger protein 141 NM_16422 Hs00212656_m1 2.17 2.37 1.62 10-6 SELENBP1 Selenium binding protein 1 NM_003944 Hs00187625_m1 2.8 1.92 .002 SFXN1 Sideroflexin 1 NM_022754 Hs00224259_m1 3 1.6 .022 SHPRH SNF2 histone-linker PHD RING NM_173082 Hs00542737_m1 3.35 1.77 .05 helicase SNAP23 Synaptosomal-associated protein, 23 NM_003825 Hs00187075_m1 1.9 2.02 .00018 kDa SORL1 Sortilin-related receptor, L(DLR class) NM_003105 Hs00268342_m1 1.57 1.54 4.10 10-8 A repeats-containing SOS1 Son of sevenless homolog 1 NM_005633 Hs00362308_m1 1.6 2.31 .002 (Drosophila) TAF11 TAF11 RNA polymerase II, TATA NM_005643 Hs00194573_m1 3.1 1.87 .05 box-binding protein (TBP)-associated factor, 28 kDa TCF3 Transcription factor 3 (E2A NM_003200 Hs00413032_m1 1.8 1.44 .023 immunoglobulin enhancer binding factors E12/E47) TDP1 Tyrosyl-DNA phosphodiesterase 1 NM_018319 Hs00217832_m1 2.1 1.67 .0099 TNFRSF1A Tumor necrosis factor receptor NM_001065 Hs00533560_m1 1.46 1.37 .016 superfamily, member 1A UBTF Upstream binding transcription NM_014233 Hs00610729_g1 1.95 2.26 .024 factor, RNA polymerase I USP38 Ubiquitin-specific peptidase 38 NM_032557 Hs00261419_m1 3.3 1.71 .0021 WAPAL Wings apart-like homolog NM_015045 Hs00386162_m1 1.97 1.69 .027 (Drosophila) WDR26 WD repeat domain 26 NM_025160 Hs00228535_m1 2.12 2.62 .00012 Transcription factor NFKB1 nuclear factor of kappa light NM_003998 Hs00231653_m1 2.8 1.59 4.04 10-5 polypeptide gene enhancer in B cells 1 (p105) NHLH1 Nescient helix loop helix 1 NM_005589 Hs00271582_s1 NA 11.51 7.00 10-4 REPIN1 Replication initiator 1 NM_013400 Hs00274221_s1 NA 3.62 6.00 10-6 GABPA GA binding protein transcription NM_002031 Hs00745591_s1 NA 8.06 3.00 10-4 factor, alpha subunit, 60 kDa ETS1 v-ets erythroblastosis virus E26 NM_005238 Hs00901425_m1 NA 2.11 1.00 10-5 oncogene homolog 1 (avian) EGR1 Early growth response 1 NM_001955 Hs00152928_m1 NA 2.82 .015 EGR3 Early growth response 3 NM_004421 Hs00231780_m1 NA 1.92 .017 ------------------------------------------------------------------------------------------------------------------ NOTE. A graphic representation of these data appears in figure 1. Fold differences are defined as the relative quantity of mRNA transcripts for patients with CFS/ME divided by the value for healthy control subjects. NA, not available; PCR, polymerase chain reaction. a Assays were predesigned by Applied Biosystems. b Genes found in pilot study [13]. c Genes found by means of differential display polymerase chain reaction [7].