Supporting Information for Proteomics DOI 10.1002/pmic.200600056
Barbara Celegato, Daniele Capitanio, Mario Pescatori, Chiara Romualdi, Beniamina Pacchioni, Stefano Cagnin, Agnese Vigan , Luca Colantoni, Shajna Begum, Enzo Ricci, Robin Wait, Gerolamo Lanfranchi and Cecilia Gelfi
Parallel protein and transcript profiles of FSHD patient muscles correlate to the D4Z4 arrangement and reveal a common impairment of slow to fast fibre differentiation and a general deregulation of MyoD-dependent genes
ª 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Table A. List of genes discriminating among the two classes of patients with the same range of size deletion (EcoRI fragment > 21Kb), but differing by age at biopsy. NA: not available value.
Table B. Mass spectrometry data of up and down regulated proteins of unclusterised patients, as shown in Figure 3.
Table C. Mass spectrometry data of up and down regulated proteins of patients after gene transcripts cluster analysis.
Table D. Common altered genes in FSHD muscle compared to a deltoideous control muscle are listed according to their biological process.
Table E. Functionally classified transcripts with an increasing profile according to KpnI repeats number at D4Z4 locus. Single patient ratios and intra-class averaged ratios are reported.
Table F. Functionally classified transcripts with a decreasing profile according to KpnI repeats number at D4Z4 locus. Single patient ratios and intra-class averaged ratios are reported.
Table G. Ratios values of selected transcripts altered in FSHD muscle, suggesting an enrichment in slow-oxidative fibers in the most severely affected patients.
Table H. MyoD target genes with an altered expression in FSHD muscle.
Figure A. Hierarchical cluster analysis of the transcriptional expression profiles of 11 FSHD patients. Profiles were obtained using the Human Muscle Array 2.0 platform, which contains 4.801 muscle cDNA probes and are expressed as FSHD deltoid/control. Pearson correlation was used as distance measure. Statistical support for the nodes of the dendrogram is also shown in figure 1A and it is expressed as a fold number percent of a given node over the resampling trials. We chose the bootstrapping genes resampling procedure to build experiment dendrogram and 500 iterations.
Patients are clearly divided into 4 groups, according to their EcoRI fragment length. Furthermore, patients with fragment longer than 20kb and age at biopsy >50 years (mean 57.7 +/- 10) are separated from younger (mean 25.7 +/- 5) patients with a comparable fragment size. Below, an enlargement of the global dendrogram showing a selection of the genes discriminating among the classes of patients.
Figure B. Percent of differentially expressed genes in each class of FSHD patients, grouped by their biological function. Note that some functional categories are specifically affected in one class of patients.
Figure C. Correlation between protein and transcript expression levels of myosin heavy chains
(MYH1, MYH7, MYH2) averaged among patients of the same class.
Table A
Human Muscle Array 2.0 Expression ratios (FSHD/control) Averaged expression ratios Gene name and biological process Chr pos Archive ID Group A Group > 50 years Group A Group > 50 years 4 - 23 Kb 3 - 26 Kb 6 - 21 Kb 1 - 27 Kb 5 - 23 Kb 2 - 27 Kb Frgm > 21Kb Oxidative phosphorilation 2-001A09 cytochrome c oxidase subunit VIa, pol 2 (COX6A2) 16 -1.18 -1.18 1.09 1.2 1.18 1.14 -1.08 1.18 2-001G05 cytochrome c oxidase subunit VIIb (COX7B) X -1.04 -1.2 -1.01 1.24 1.1 1.11 -1.08 1.15 2-003E10 NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 1 (NDUFC1) 4 -1.11 -1.19 1.06 1.03 -1.05 1.25 -1.07 1.08 Protein biosynthesis 2-001D07 ribosomal protein S18 (RPS18) 6 -1.12 -1.23 1.14 -1 1.02 1.22 -1.05 1.08 2-001G01 ribosomal protein S8 (RPS8) 1 -1.08 -1.14 1.15 1.15 1.11 1.11 -1.02 1.12 2-018H06 mitochondrial ribosomal protein L46 (MRPL46) 15 -1.22 -1.22 -1.11 1.06 1.06 1.1 -1.18 1.07 2-018H02 aspartyl aminopeptidase (DNPEP) 2 -1.14 -1.14 -1.07 1.01 1.18 1.14 -1.12 1.11 Proteolysis 2-017D05 ubiquitin protein ligase E3A (UBE3A) 15 -1.33 -1.33 1.05 1.09 1.15 1.08 -1.18 1.1 2-029A02 cathepsin B (CTSB) 8 2.01 2.25 2.1 -2 -1.76 -1.94 2.12 -1.89 2-033C05 KIAA0317 gene product 14 2.35 1.89 2.11 -1.9 -1.42 -1.64 2.12 -1.63 Muscle contraction 2-008A02 creatine kinase, muscle (CKM) 19 -1.25 -1.16 -1.06 1.04 1.18 1.11 -1.15 1.11 2-021E11 tropomyosin 2 (beta) 9 2.35 2.19 1.9 -1.72 -1.4 -1.39 2.15 -1.49 2-021C11 tropomyosin 2 (beta) 9 2.29 1.95 1.82 -1.48 -1.56 -1.45 2.02 -1.49 2-001A05 titin-cap (telethonin) (TCAP) 17 2.28 1.88 1.84 -1.93 -1.33 -1.79 2 -1.64 2-010H06 troponin C2, fast (TNNC2) 20 -1.24 -1.2 -1.05 1.01 1.2 1.16 -1.16 1.12 2-022B02 troponin I, skeletal, fast (TNNI2) 11 2.7 1.95 1.64 -2.21 -1.22 -1.46 2.09 -1.53 2-024D08 troponin T1, skeletal, slow (TNNT1) 19 3.55 2.51 2.3 -2.23 -1.38 -2.18 2.79 -1.84 2-024F02 troponin T1, skeletal, slow (TNNT1) 19 3.04 2.99 1.82 -2.22 -1.37 -2.03 2.62 -1.79 2-023F09 troponin T1, skeletal, slow (TNNT1) 19 3.2 3.07 2.31 -2.09 -1.19 -2.02 2.86 -1.66 2-021E03 troponin T1, skeletal, slow (TNNT1) 19 3.35 2.35 1.88 -1.91 -1.44 -2.16 2.53 -1.79 2-023H12 troponin T1, skeletal, slow (TNNT1) 19 3.11 3.12 1.67 -1.85 -1.13 -1.68 2.64 -1.49 2-001A12 troponin T1, skeletal, slow (TNNT1) 19 2.43 2.17 1.72 -1.2 -1.35 -1.6 2.11 -1.37 2-020A10 troponin T3, skeletal, fast (TNNT3) 11 4.86 5.51 4.03 -2.56 -2.16 -1.62 4.8 -2.04 2-001H06 troponin T3, skeletal, fast (TNNT3) 11 4.6 5.46 3.84 -2.11 -1.49 -1.37 4.63 -1.6 Cell cycle control 2-008G02 zinc finger, HIT domain containing 1 7 -1.09 -1.12 -1.09 1.06 1.15 1.12 -1.1 1.11 2-007F05 protein phosphatase 2A, regulatory subunit B (PR 53) 9 -1.13 -1.2 1 1.11 1.13 1.18 -1.1 1.14 BL-007F08 retinoblastoma binding protein 7 (RBBP7) X -1.11 -1.16 1.01 1.11 1.21 1.23 -1.08 1.19 Apoptosis BL-001B06 BH3 interacting domain death agonist (BID) 22 -1.14 -1.17 1.03 1.03 NA 1.17 -1.09 1.1 2-029A02 cathepsin B (CTSB) 8 2.01 2.25 2.1 -2 -1.76 -1.94 2.12 -1.8 Regulation of transcription 2-011H11 transcription factor LZIP mRNA (CREB3) 9 -1.13 -1.15 -1.1 1.03 1.22 1.19 -1.12 1.15 2-029C02 myocyte enhancer factor 2C (MEF2C) 5 -1.35 -1.36 -1.45 1.06 1.03 1.18 -1.39 1.09 Extracellular matrix 2-025E09 laminin, alpha 4 (LAMA4) 6 4.76 4.51 3.36 -1.77 -1.76 -1.5 4.21 -1.67 2-016C10 laminin, beta 2 (laminin S) (LAMB2) 3 -1.22 -1.22 -1.01 1.14 1.12 1.16 -1.14 1.14 Other 2-009A04 lamin B1 (LMNB1) 5 -1.3 -1.15 1.08 1.06 1.03 1.12 -1.1 1.07 2-015F09 voltage-dependent anion channel 2 (VDAC2) 10 -1.13 -1.23 1.04 1.19 1.26 1.18 -1.09 1.21 2-018H10 PDZ and LIM domain 2 (mystique) 8 -1.18 -1.31 -1.12 1.15 1.21 1.17 -1.2 1.18 2-003B09 monoglyceride lipase 3 -1.16 -1.26 -1.01 1.08 1.28 1.2 -1.14 1.19 2-016G12 B-cell associated protein (REA) 12 -1.01 -1.27 -1.01 1.21 1.08 1.18 -1.08 1.16 2-016B11 coatomer protein complex, subunit epsilon (COPE) 19 -1.27 -1.22 -1.01 1.2 1.24 1.22 -1.15 1.22 BL-002H11 arachidonate 5-lipoxygenase-activating protein (ALOX5AP) 13 -1.14 -1.2 -1.08 1.12 1.04 1.18 -1.14 1.11 BL-002F03 sorting nexin 17 2 -1.17 -1.15 -1.04 -1.01 1.17 1.1 -1.12 1.09 BL-003H07 formin-like (FMNL) 17 -1.09 -1.17 -1.12 1.06 1.16 1.16 -1.12 1.12 2-029G06 SNARE associated protein snapin 1 -1.19 -1.11 -1.07 -1.04 1.1 1.11 -1.12 1.06 2-012D10 SEC13-like 1 3 -1.21 -1.41 -1.02 1.1 1.18 1.22 -1.19 1.16 Unknown 2-017E07 haloacid dehalogenase-like hydrolase domain containing 1A (GS1) X -1.09 -1.16 1.1 1.16 1.18 1.03 -1.04 1.12 2-005A01 aurora-A kinase interacting protein (AKIP) 1 -1.06 -1.24 1.1 1.22 1.1 1.12 -1.05 1.15 BL-002B09 hypothetical protein LOC51234 15 -1.1 -1.27 1.06 -1.03 -1 1.21 -1.09 1.06 2-008F10 unknown seqeunce from clone RP11-545E24 1 -1.21 -1.38 -1.02 1.15 1.18 1.2 -1.18 1.18 2-017C01 unknown seqeunce from clone CTD-2545M3 19 -1.33 -1.49 -1.04 1.02 1.06 1.19 -1.26 1.09 2-013D10 hypothetical protein FLJ10769 (FLJ10769) 13 -1.19 -1.37 -1.01 1.08 1.12 1.12 -1.17 1.11 2-001H10 ankyrin repeat domain 23 2 -1.31 -1.29 -1.12 -1.01 -1 -1.02 -1.23 -1.01 2-033G02 unknown sequence from PAC clone RP4-745K6 17 -1.15 -1.24 1.17 1.19 1.25 1.08 -1.05 1.17 2-017B04 chromosome 5 open reading frame 13 5 -1.24 -1.3 1.08 1.02 1.08 1.04 -1.13 1.05 2-020D03 SCIRP10-related protein 1 5.2 6.19 4.14 -1.73 -1.84 -1.57 5.17 -1.71 BL-002B05 zinc finger, ZZ domain containing 3 (ZZZ3) 1 -1.11 -1.2 -1.11 1.04 1.14 1.15 -1.14 1.11 2-012H02 chromosome 20 open reading frame 111 20 -1.13 -1.28 -1.02 1.11 1.14 1.18 -1.13 1.14 2-011G09 chromosome 2 open reading frame 24 2 NA -1.4 1.12 1.11 1.11 1.19 -1.09 1.14 2-005C06 hypothetical gene supported by BC055092 8 2.34 2.85 1.8 -1.55 -1.44 NA 2.33 -1.49 2-005F01 selenoprotein O 22 -1.05 -1.19 -1.05 1.15 1.14 1.15 -1.09 1.15
Table B
FSHD Upregulated proteins: Swissprot/ MW (Da) MW (Da) TrEMBL pI using pI using calculated Spot Spot AC ExPASy calculated ExPASy from 2D- volume volume log2 spot N° Number Protein p-value tool from 2D-gel tool gel Control FSHD (FSHD/Control)
Contraction/structur al proteins: 201 P02675 Fibrinogen beta chain precursor 0.006 8.54 8.50 55 928.15 52 673 0.043 0.073 0.76 99 O75083 WD repeat prot, 1 0.018 6.17 6.99 66 193.52 69 178 0.003 0.004 0.42
Anaerobic metabolism: 191 P00352 Aldehyde DH 1A1 0.006 6.29 6.94 54 730.65 53 304 0.039 0.097 1.31 248 P06733 Alpha enolase 0.008 6.99 7.07 47 037.77 46 415 0.159 0.219 0.46 331 P17174 Aspartate aminotransferase, cytoplasmic 0.004 6.57 7.64 46 116.31 39 931 0.059 0.111 0.91 323 P17174 Aspartate aminotransferase, cytoplasmic 0.004 6.57 7.70 46 116.31 40 573 0.09 0.15 0.74 271 P13929 Beta enolase < 10 -3 7.73 7.79 46 855.69 44 719 0.119 0.234 0.98 272 P13929 Beta enolase 0.018 7.73 8.06 46 855.69 44 676 0.071 0.115 0.70 273 P13929 Beta enolase 0.003 7.73 8.36 46 855.69 44 590 0.323 0.494 0.61 275 P13929 Beta enolase < 10 -3 7.73 8.48 46 855.69 44 463 0.804 1.587 0.98 292 P06732 Creatine kinase, M chain 0.011 6.77 8.48 43 101.12 42 387 0.128 0.205 0.68 293 P06732 Creatine kinase, M chain 0.005 6.77 8.52 43 101.12 42 317 0.083 0.137 0.72 302 P06732 Creatine kinase, M chain 0.026 6.77 7.22 43 101.12 41 743 0.184 0.27 0.55 346 P04075 Fructose-bisphosphate aldolase A 0.02 8.39 8.55 39 288.83 39 410 0.918 1.165 0.34 348 P04075 Fructose-bisphosphate aldolase A 0.004 8.39 8.66 39 288.83 39 284 1.669 2.59 0.63 409 P04406 Glyceraldehyde-3-phosphate DH 0.005 8.58 8.53 35 922.02 36 176 0.556 0.835 0.59 412 P04406 Glyceraldehyde-3-phosphate DH < 10 -3 8.58 8.63 35 922.02 36 059 0.905 1.482 0.71 415 P04406 Glyceraldehyde-3-phosphate DH 0.024 8.58 8.80 35 922.02 36 020 2.584 3.579 0.47 8 P11217 Glycogen phosphorylase muscle form 0.004 6.57 7.58 96 960.86 98 879 0.008 0.021 1.39 10 P11217 Glycogen phosphorylase muscle form 0.038 6.57 7.38 96 960.86 98 541 0.296 0.351 0.25 450 P00338 L-lactate dehydrogenase A chain 0.018 8.46 8.66 36 557.53 34 749 2.083 2.78 0.42 113 P36871 Phosphoglucomutase 0.02 6.32 6.30 61 317.93 64 478 0.004 0.009 1.17 114 P36871 Phosphoglucomutase 0.03 6.32 7.00 61 317.93 64 178 0.067 0.103 0.62 116 P36871 Phosphoglucomutase 0.002 6.32 7.33 61 317.93 63 979 0.028 0.037 0.38 118 P36871 Phosphoglucomutase 0.012 6.32 6.83 61 317.93 63 682 0.072 0.104 0.53 120 P36871 Phosphoglucomutase 0.009 6.32 6.68 61 317.93 63 289 0.018 0.041 1.19 122 P36871 Phosphoglucomutase 0.045 6.32 6.19 61 317.93 62 802 0.008 0.02 1.32 563 P15259 Phosphoglycerate mutase, muscle form 0.003 9 8.71 28 634.98 29 047 0.323 0.367 0.19 143 P14618 Pyruvate kinase, M1 isozyme < 10 -3 7.95 8.42 57 805.70 59 187 0.132 0.236 0.84 144 P14618 Pyruvate kinase, M1 isozyme 0.001 7.95 8.47 57 805.70 59 187 0.506 0.745 0.56 219 Q16851 UTP-glucose-1-phosphate uridylyltransferase 2 0.002 7.69 8.44 55 676.78 51 399 0.104 0.165 0.67
Oxidative metabolism: 28 Q99798 Aconitate hydratase, mitochondrial precursor 0.024 7.36 8.35 85 425.41 88 988 0.039 0.056 0.52 31 Q99798 Aconitate hydratase, mitochondrial precursor 0.014 7.36 8.39 85 425.41 88 736 0.13 0.175 0.43 27 Q99798 Aconitate hydratase, mitochondrial precursor 0.04 7.36 8.48 85 425.41 89 239 0.009 0.033 1.90 544 P07451 Carbonic anhydrase III 0.03 6.94 7.91 29 440.26 29 833 0.389 0.596 0.62 Dihydrolipoamide dehydrogenase mitochondrial 175 P09622 precursor 0.001 7.59 7.92 54 150.18 55 072 0.082 0.144 0.81 Dihydrolipoamide dehydrogenase mitochondrial 189 P09622 precursor 0.005 7.59 7.89 54 150.18 53 518 0.005 0.01 1.00 422 P40925 Malate DH citoplasmic 0.017 6.89 6.72 36 294.93 35 824 0.124 0.133 0.10 426 P40925 Malate DH citoplasmic < 10 -3 6.89 7.71 36 294.93 35 649 0.264 0.404 0.61 428 P40925 Malate DH citoplasmic < 10 -3 6.89 7.23 36 294.93 35 590 0.194 0.279 0.52 69 P28331 NADH-ubiquinone oxidoreductase 75 kDa subunit 0.002 5.89 5.31 79 515.54 78 543 0.013 0.041 1.66 492 Q16836 Short chain 3 hydroxyacil-CoA DH mitochondrial 0.043 8.88 8.67 34 277.50 32 564 0.224 0.342 0.61 491 Q16836 Short chain 3 hydroxyacil-CoA DH mitochondrial 0.002 8.88 8.55 34 277.50 32 564 0.007 0.017 1.28 493 Q16836 Short chain 3 hydroxyacil-CoA DH mitochondrial 0.002 8.88 8.76 34 277.50 32 487 0.37 0.611 0.72 289 P22695 Ubiquinol-cytochrome c reductase core protein 1 < 10 -3 8.74 8.63 48 443.01 42 564 0.271 0.589 1.12
Transport: 48 P02787 Serotransferrin precursor < 10 -3 6.81 6.93 77 049.87 84 252 0.087 0.137 0.66
DNA/Protein synthesis: 264 P49411 Elongation factor Tu, mitochondrial precursor 0.002 7.26 7.07 49 541.54 45 246 0.073 0.125 0.78
Signalling/regulatory proteins: 200 P40123 Adenylyl cyclase associated protein 2 0.025 5.95 5.98 52 823.96 52 742 0.021 0.039 0.86
Stress resistance proteins: 680 P04792 Heat shock 27 kDa protein family, member 7 0.027 5.98 5.68 22 782.52 19 988 0.042 0.045 0.09
FSHD Downregulated proteins:
SwissProt- MW (Da) MW (Da) TrEMBL pI using pI using calculated Spot Spot AC ExPASy calculated ExPASy from 2D- volume volume log2 spot N° Number Protein p-value tool from 2D-gel tool gel Control FSHD (FSHD/Control)
Contraction/structur al proteins: 327 P02568 Actin alpha skeletal muscle 0.029 5.23 5.57 42 018.97 40 288 0.085 0.052 -0.71 325 P04270 Actin, alpha cardiac 0.023 5.23 5.41 42 051.03 40 515 0.204 0.157 -0.38 396 P04270 Actin, alpha cardiac 0.001 5.23 5.34 42 051.03 36 391 0.109 0.06 -0.86 684 P02511 Alpha cristallin B chain 0.009 6.76 8.39 20 158.91 19 738 0.293 0.272 -0.11 697 P02511 Alpha cristallin B chain, Heat-shock protein beta-5 0.002 6.76 5.20 20 158.91 18 273 0.051 0.019 -1.42 371 Q9GZV1 Ankyrin repeat domain protein 2 0.023 5.71 5.35 37 151.08 38 427 0.018 0.014 -0.28 689 P23528 Cofilin 0.027 8.22 8.55 18 502.49 19 188 0.033 0.016 -1.04 220 P17661 Desmin 0.046 5.21 5.28 53 404.60 51 269 0.014 0.006 -1.22 447 P47755 F-actin capping protein alpha-2 subunit < 10 -3 5.58 5.18 32 817.92 32 024 0.056 0.021 -1.42 455 P47755 F-actin capping protein alpha-2 subunit 0.003 5.58 5.26 32 817.92 32 043 0.013 0.006 -1.12 504 P47756 F-actin capping protein beta subunit 0.004 5.36 5.48 31 219.30 34 866 0.009 0.005 -0.85 503 P47756 F-actin capping protein beta subunit < 10 -3 5.36 5.34 31 219.30 34 651 0.051 0.012 -2.09 169 P05217 Tubulin beta 2 chain 0.001 4.79 4.84 49 831.01 55 847 0.051 0.018 -1.50
Anaerobic metabolism: 295 P06732 Creatine kinase, M chain 0.006 6.77 8.45 43 101.12 42 145 0.359 0.273 -0.40 411 P04406 Glyceraldehyde-3-phosphate DH 0.001 8.58 8.58 35 922.02 36 156 0.242 0.105 -1.20 110 P36871 Phosphoglucomutase 0.001 6.32 6.83 61 317.93 66 108 0.018 0.007 -1.36
Oxidative metabolism: 234 P06576 ATP-synthase beta chain, mitochondrial precursor 0.045 5.26 5.02 56 559.90 48 448 0.079 0.041 -0.95 569 P30084 Enoyl CoA hydratase, mitochondrial precursor 0.022 8.34 5.86 31 371.39 28 671 0.061 0.044 -0.47
Transport: 613 P02647 Apolipoprotein A-I prec, 0.024 5.57 5.21 30 777.83 26 524 0.019 0.010 -0.93 615 P02647 Apolipoprotein A-I prec, 0.004 5.57 5.27 30 777.83 26 491 0.227 0.105 -1.11 708 P05413 Fatty acid binding protein 0.001 6.34 5.41 14 726.84 16 693 0.049 0.029 -0.76 93 P02768 Serum albumin precursor 0.031 5.92 5.74 69 366.68 70 159 2.339 1.813 -0.37 546 Q9Y277 Voltage-dependent anion-selective channel < 10 -3 8.84 8.95 30 658.66 29 685 0.046 0.040 -0.21
DNA/Protein synthesis: 40S ribosomal prot, SA, p40, 34/67 kDa laminin 335 P08865 receptor 0.036 4.79 4.86 32 722.88 39 851 0.008 0.004 -1.00 98 P08107 HSP70 prot, 1 0.004 5.48 5.31 70 052.23 69 395 0.091 0.044 -1.05 100 P08107 HSP70 prot, 1 < 10 -3 5.48 5.34 70 052.23 69 070 0.306 0.164 -0.90 540 Q9Y235 Probable c-->u editing enzyme APOBEC 2 0.001 4.81 4.99 25 703.14 30 092 0.08 0.022 -1.86 541 P35232 Prohibitin 0.018 5.57 5.35 29 804.10 30 018 0.026 0.015 -0.79 595 P52565 Rho GDP-dissociation inhibitor 1 < 10 -3 5.03 5.07 23 207.11 27 724 0.018 0.004 -2.17
Degradation/oxidativ e stress: 171 P01009 Alpha-1-antitrypsin precursor 0.049 5.37 5.01 46 736.55 55 769 0.306 0.214 -0.52 153 P01009 Alpha-1-antitrypsin precursor 0.013 5.37 5.06 46 736.55 57 890 0.028 0.007 -2.00 601 P28161 Glutathione S-transferase Mu 2 0.007 6.02 6.27 25 613.46 27 109 0.072 0.05 -0.53 651 P32119 Peroxiredoxin 2 0.048 5.66 5.27 21 891.92 24 382 0.104 0.04 -1.38 527 Q9UL46 Proteasome activator complex, subunit 2 0.001 5.44 5.31 27 361.61 30 559 0.011 0.004 -1.46 686 P00441 Superoxide dismutase 0.002 5.7 5.36 15 804.55 19 545 0.013 0.004 -1.70 685 P00441 Superoxide dismutase 0.019 5.7 5.61 15 804.55 19 656 0.097 0.061 -0.67 653 P04179 Superoxide dismutase, mitochondrial precursor 0.047 8.35 8.29 24 722.09 24 259 0.12 0.082 -0.55
Signalling/regulatory proteins: 517 P62258 14-3-3 protein epsilon 0.005 4.63 4.72 29 173.90 30 973 0.013 0.005 -1.38 340 Q9BT78 COP9 subunit 4 < 10 -3 5.57 5.42 46 268.81 39 589 0.024 0.008 -1.58
Other proteins: 677 O14558 Heat shock 20 kDa like-protein P20 0.035 5.95 6.02 17 135.60 20 447 0.162 0.112 -0.53 464 O75208 O75208 Hypotetical protein 0.019 5.61 5.07 35 508.99 34 338 0.01 0.006 -0.74 463 O75208 O75208 Hypotetical protein 0.042 5.61 5.14 35 508.99 34 357 0.007 0.004 -0.81
Table C
log2 (FSHD/Control) Swissprot/TrEMBL Spot N° AC number Protein Group A Group B Group C Contraction/structural proteins: 396 P04270 Actin, alpha cardiac -1.2 -0.4 -1.0 579 P04270 Actin, alpha cardiac 0.7 1.1 0.1 312 P04270 Actin, alpha cardiac -0.7 -0.7 -0.8 684 P02511 Alpha cristallin B chain -0.6 -0.2 0.3 697 P02511 Alpha cristallin B chain -2.0 -1.3 -0.8 371 Q9GZV1 Ankyrin repeat domain protein 2 -0.4 0.2 -0.8 447 P47755 F-actin capping protein alpha-2 subunit -1.8 -1.0 -1.3 455 P47755 F-actin capping protein alpha-2 subunit -1.0 -1.6 -0.5 503 P47756 F-actin capping protein beta subunit -2.1 -1.8 -1.8 Oxidative metabolism: 39 Q99798 Aconitate hydratase, mitochondrial precursor 1.2 1.1 1.7 40 Q99798 Aconitate hydratase, mitochondrial precursor 1.6 1.1 2.0 27 Q99798 Aconitate hydratase, mitochondrial precursor 1.6 1.7 2.3 544 P07451 Carbonic anhydrase III P07451 0.8 0.5 -0.2 189 P09622 Dihydrolipoamide dehydrogenase mitochondrial precursor 1.2 0.6 0.8 175 P09622 Dihydrolipoamide dehydrogenase mitochondrial precursor 0.7 0.5 1.2 422 P40925 Malate DH citoplasmic -0.4 0.4 0.2 426 P40925 Malate DH citoplasmic 0.3 0.5 0.8 428 P40925 Malate DH citoplasmic -0.3 0.6 1.0 69 P28331 NADH-ubiquinone oxidoreductase 75 kDa subunit 1.3 1.3 1.3 491 Q16836 Short chain 3 hydroxyacil-CoA DH mitochondrial 0.5 0.6 0.4 289 P22695 Ubiquinol-cytochrome c reductase core protein 1 0.9 1.2 1.1 Anaerobic metabolism: 191 P00352 Aldehyde DH 1A1 1.2 1.3 1.1 248 P06733 Alpha enolase 0.2 0.3 0.7 331 P17174 Aspartate aminotransferase, cytoplasmic 0.9 0.9 -0.1 271 P13929 Beta enolase 1.0 0.8 1.0 272 P13929 Beta enolase 0.8 0.3 0.3 273 P13929 Beta enolase 0.7 0.5 0.4 275 P13929 Beta enolase 1.0 0.8 0.8 292 P06732 Creatine kinase, M chain 1.0 0.0 -0.1 293 P06732 Creatine kinase, M chain 0.8 0.6 -0.2 295 P06732 Creatine kinase, M chain 0.1 -0.7 -0.8 348 P04075 Fructose-bisphosphate aldolase A 0.5 0.7 0.2 409 P04406 Glyceraldehyde-3-phosphate DH 0.4 0.7 0.5 412 P04406 Glyceraldehyde-3-phosphate DH 0.5 0.6 0.8 411 P04406 Glyceraldehyde-3-phosphate DH -1.3 -2.7 -0.8 8 P11217 Glycogen phosphorylase muscle form 1.3 0.8 1.6 10 P11217 Glycogen phosphorylase muscle form 0.1 0.5 0.1 450 P00338 L-lactate dehydrogenase A chain 0.2 0.0 0.6 110 P36871 Phosphoglucomutase -1.0 -0.6 -0.3 113 P36871 Phosphoglucomutase 0.6 1.6 1.3 114 P36871 Phosphoglucomutase 0.9 0.2 0.6 116 P36871 Phosphoglucomutase -2.1 1.0 0.7 118 P36871 Phosphoglucomutase 0.3 -1.8 1.5 120 P36871 Phosphoglucomutase 0.9 1.6 0.4 122 P36871 Phosphoglucomutase 1.7 -0.2 -0.9 563 P15259 Phosphoglycerate mutase, muscle form -0.5 0.3 0.6 143 P14618 Pyruvate kinase, M1 isozyme 0.6 0.9 0.6 144 P14618 Pyruvate kinase, M1 isozyme 0.4 0.6 0.4 219 Q16851 UTP-glucose-1-phosphate uridylyltransferase 2 0.7 0.7 0.1 Transport: 615 P02647 Apolipoprotein A-I prec. -0.6 -1.2 -2.2 708 P05413 Fatty acid binding protein -0.4 -0.4 -1.6 48 P02787 Serotransferrin prec. 0.8 0.5 0.6 546 Q9Y277 Voltage-dependent anion- selective channel -0.8 -1.1 0.6 DNA/Protein synthesis: 98 P08107 HSP70 prot.1 -1.0 -0.8 -2.2 100 P08107 HSP70 prot.1 -0.7 -0.9 -1.7 540 Q9Y235 Probable c-->u editing enzyme APOBEC 2 -2.2 -1.6 -1.4 595 P52565 Rho GDP-dissociation inhibitor 1 -2.5 -1.6 -1.5 Signalling/regulatory proteins: 200 P40123 Adenylyl cyclase associated protein 2 0.0 0.7 1.5 340 Q9BT78 COP9 signalosome subunit 4 -1.7 -1.6 -1.3 Stress resistance proteins: 680 P04792 Heat shock 27 kDa protein family, member 7 -0.7 0.0 0.7 Degradation/oxidative stress: 685 P00441 Superoxide dismutase -0.8 -0.3 -1.7 686 P00441 Superoxide dismutase -2.5 -1.3 -2.5 Other proteins: 677 O14558 Heat shock 20 kDa like-protein P20 -1.0 0.0 -0.5
Table D
Human Averaged expression Chr Muscle Gene name and biological process Expression ratios (FSHD/control) ratios Array 2.0 pos Archive ID Group A Group B Group C A B C 21Kb < Frgm > Frgm > Frgm = 3-26 kb 4-23 Kb 6-21 Kb 7-19 Kb 8-16 Kb 9-10 Kb 10-10 Kb 11-10 Kb 21Kb 16Kb 10Kb Oxidative phosphorilation 2-022D11 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7 (NDUFB7) 19 NA NA 1.8 1.25 1 1.51 1.42 1.57 1.8 1.13 1.5 2-021H06 cytochrome c oxidase subunit VIIc 5 -1.38 -1.53 -1.48 1.09 -1.05 -1.45 -1.24 -1.46 -1.46 1.02 -1.38 Transcripts codified by mitochondrial genome 2-041C03 ATP synthase F0 subunit 6 (ATP6) 1.95 1.84 1.15 1.81 NA 1.15 1.86 1.52 1.65 1.81 1.51 2-041D09 cytochrome b (cytb) 2.21 2.2 1.46 NA 1.39 1.62 1.76 1.63 1.96 1.39 1.67 2-041C02 cytochrome oxidase subunit II (COX2) 2.88 2.22 1.13 NA 2.06 1.94 2.21 1.89 2.08 2.06 2.01 2-041C01 cytochrome oxidase subunit II (COX2) 2.94 1.7 1.18 1.43 2.38 1.86 1.98 1.81 1.94 1.9 1.88 2-041B02 NADH dehydrogenase subunit 1 1.39 1.47 1.41 NA 1.26 1.54 1.85 1.35 1.43 1.26 1.58 2-041B01 NADH dehydrogenase subunit 1 2.15 NA 1.28 NA 1.16 1.48 1.58 1.45 1.71 1.16 1.5 2-041B04 NADH dehydrogenase subunit 2 1.56 1.38 1.3 1.33 1.09 1.12 1.41 1.25 1.41 1.21 1.26 2-041C12 NADH dehydrogenase subunit 4 1.83 1.93 1.15 1.4 NA 1.33 2.03 1.38 1.64 1.4 1.58 Protein biosynthesis 2-002E07 ribosomal protein L23 (RPL23) 17 NA -1.02 1.23 1.99 NA 1.23 1.48 1.1 1.11 1.99 1.27 2-026F11 mitochondrial ribosomal protein S18-2 (MRPS18-2) 6 NA 1.58 -1.08 1.13 2.55 1.73 1.25 1.79 1.26 1.84 1.59 2-030G04 mitochondrial ribosomal protein L23 (MRPL23) 11 NA -1.11 -1.07 -1.48 -1.49 -1.65 -1.27 -1.14 -1.09 -1.49 -1.32 2-026G01 ribosomal protein S27-like 15 NA NA -1.48 -1.08 -1.01 -1.32 -1.3 -1.47 -1.48 -1.04 -1.36 2-028E11 ribosome binding protein 1 homolog 180kDa (RRBP1) 20 1.14 1.15 1.12 1.52 1.56 1.83 1.28 1.51 1.14 1.54 1.54 Proteolysis 2-035D08 ubiquitin-like 4 (UBL4) X 1.25 NA 1.67 1.59 1.36 1.88 1.26 1.34 1.46 1.48 1.49 2-029A02 cathepsin B (CTSB) 8 2.25 2.01 2.1 -1.19 1.46 1.48 1.21 2.11 2.12 1.15 1.6 2-016G11 neural precursor cell expressed, developmentally down-regulated 8 (NEDD8) 14 NA NA 1.05 1.41 2.07 1.22 1.18 1.19 1.05 1.74 1.19 2-035C07 ring finger protein 26 (RNF26) 11 NA NA 1.65 1.21 1.77 1.38 1.23 1.23 1.65 1.49 1.28 Muscle contraction 2-022F10 myoglobin (MB) 22 NA 1.9 1.62 1.46 2.06 2.08 1.8 1.65 1.76 1.76 1.84 2-024C11 myosin, light polypeptide 3, alkali; ventricular, skeletal, slow (MYL3) 3 1.62 NA 1.39 1.22 1 1.5 1.35 1.49 1.51 1.11 1.44 2-022F08 myosin, light polypeptide 3, alkali; ventricular, skeletal, slow (MYL3) 3 1.72 1.99 1.41 1.2 NA 1.82 1 1.47 1.71 1.2 1.43 2-023E04 myosin, light polypeptide 3, alkali; ventricular, skeletal, slow (MYL3) 3 2 NA 1.82 1.12 NA 1.91 1.46 1.85 1.91 1.12 1.74 Cell cycle control 2-015H04 cyclin I (CCNI) 4 NA NA -1.46 -1.96 -1.16 -1.15 -1.1 -1.38 -1.46 -1.45 -1.2 2-031E05 receptor protein tyrosine kinase variant EphB4v1 (EPHB4) 7 1.96 NA 1.68 1.55 NA 1.94 1.36 1.7 1.82 1.55 1.67 2-031H12 pleiotrophin (heparin binding growth factor 8, neurite growth-promoting factor 1) 7 1.6 NA 1.78 NA 2.83 2.24 4.5 2.06 1.69 2.83 2.93 BL-006C06 cell division cycle and apoptosis regulator 1 (CCAR1 or CARP1) 10 -1.87 -1.04 NA -1.71 -1.48 -1.49 -1.12 -1.1 -1.34 -1.58 -1.21 Regulation of transcription TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 55 kD BL-003B05 (TAF7) 5 NA -1.23 -1.45 NA -1.29 -1.48 -1.3 -1.53 -1.33 -1.29 -1.43 2-031E08 retinoid X receptor, beta (RXRB) 6 2.24 1.84 1.19 1.17 2.74 1.68 1.33 1.57 1.76 1.96 1.53 2-029C02 myocyte enhancer factor 2C (MEF2C) 5 -1.36 -1.35 -1.45 1 -1.22 -1.37 1.02 -1.29 -1.39 -1.1 -1.19 2-013B01 peroxisome proliferative activated receptor, alpha (PPARA) 22 1.87 1.7 1.06 1.38 2.21 1.56 1.31 1.57 1.55 1.79 1.48 Apoptosis 2-035C10 interleukin-1 receptor-associated kinase 1 (IRAK1) X 1.55 NA 1.24 1.26 3.27 1.67 2.33 2 1.4 2.27 2 2-029A02 cathepsin B (CTSB) 8 2.25 2.01 2.1 -1.19 1.46 1.48 1.21 2.11 2.12 1.15 1.6 BL-006C06 cell division cycle and apoptosis regulator 1 (CCAR1 or CARP1) 10 -1.87 -1.04 NA -1.71 -1.48 -1.49 -1.12 -1.1 -1.34 -1.58 -1.21 Signal transduction 2-026E10 ras homolog gene family, member C (RHOC) 1 2.48 1.77 1.65 -1.06 NA 1.68 1.25 1.34 1.97 -1.06 1.42 2-040H11 glucocorticoid-inducible protein or lipocalin 7 1 -1.64 -1.35 -1.01 -1.47 -1.32 -1.35 -1.86 -1.15 -1.28 -1.39 -1.39 2-029G01 polycystic kidney disease 1-like (PKD1-like) 1 -2.47 -1.21 NA -1.55 -1.4 -1.59 -1.42 -1.15 -1.63 -1.47 -1.37 2-007D10 histidine triad nucleotide-binding protein (HINT) 5 2.01 1.75 1.26 1.24 1.66 2.04 1.33 1.41 1.67 1.45 1.59 2-035C10 interleukin-1 receptor-associated kinase 1 (IRAK1) X 1.55 NA 1.24 1.26 3.27 1.67 2.33 2 1.4 2.27 2 2-029G02 ankyrin repeat and SOCS box-containing 6 (ASB6) 3 2.77 NA 1.73 NA 2.65 2.25 2.57 1.94 2.25 2.65 2.25 Other 2-027D01 sperm associated antigen 7 (SPAG7) 17 NA NA 1.52 1.24 1.05 1.2 1.19 1.25 1.52 1.14 1.21 2-014E03 heat shock 40kD protein 1 (HSPF1) 19 NA 1.84 1.5 -1 NA 1.5 1.29 1.68 1.67 -1 1.49 2-033B09 HNK-1 sulfotransferase (CHST10) 2 NA NA 1.73 NA 1.68 1.85 1.48 1.6 1.73 1.68 1.64 2-033B12 URB, steroid sensitive gene 1 3 1.78 NA 1.11 1.39 2.79 2.07 2.19 1.99 1.45 2.09 2.08 2-003H06 tumor protein, translationally-controlled 1 (TPT1) 13 -1.66 -1.35 -1.52 -1.55 1.12 -1.35 -1.46 -1.41 -1.5 -1.13 -1.4 2-038A04 cDNA DKFZp564N1063 2 NA NA 1.71 1.6 1.51 1.52 1.12 1.34 1.71 1.56 1.33 Unknown 2-025E05 nuclear ubiquitous casein kinase and cyclin-dependent kinase substrate (NUCKS) 1 NA NA -1.63 -1.01 -1.03 -1.42 -1.94 -1.27 -1.63 -1.02 -1.49 2-029E07 unknown sequence from BAC RP11-968A15 12 -1.84 -1.35 -1.39 -1.11 -1.26 -2.53 -1.35 -2.03 -1.5 -1.18 -1.84 2-031D11 hypothetical protein FLJ10305 16 2.51 NA 1.81 1.25 NA 1.74 1.51 2.24 2.16 1.25 1.83 2-030A12 unknown sequence from clone hRPK.147_L_13 17 1.91 1.95 -1.1 1.34 2.91 1.81 1.45 1.91 1.59 2.13 1.72 2-038F04 TPR domain, ankyrin-repeat and coiled-coil-containing 2 1.78 1.41 1.69 1.52 2.24 3.36 1.74 2.24 1.62 1.88 2.45 BL-003D03 unknown sequence from clone RP11-536I18 2 -2.45 -1.29 1.13 -1.19 -1.56 -1.64 -1.64 -1.37 -1.3 -1.35 -1.54 2-028E02 microtubule associated serine/threonine kinase family member 4 5 1.44 1.27 1.44 1.68 1.75 1.79 1.38 1.37 1.38 1.72 1.51 2-026A05 family with sequence similarity 20, member C (FAM20C) 7 NA NA 1.02 1.98 NA 1.49 1.67 NA 1.02 1.98 1.58 BL-009D09 unknown sequence from clone RP11-17L7 9 1.45 -1.19 NA -2.67 -1.48 -1.99 -1.47 -1.04 1.15 -1.9 -1.4
Table E
Human Muscle Array Averaged expression ratios (FSHD/control) Gene name and biological process Chr pos 2.0 Archive ID Group A Group B Group C Frgm > 21Kb 21Kb < Frgm > 16Kb Frgm = 10Kb Transcripts codified by mitochondrial genome 2-041A04 12S ribosomal RNA -1.26 1.45 1.1 2-041C07 cytochrome oxidase subunit III (COX3) -1.42 -1.19 1.84 2-041D12 cytochrome b (cytb) 1.16 1.44 1.87 2-041C05 ATP synthase F0 subunit 6 (ATP6) -1.14 -1.04 1.42 Protein biosynthesis 2-002E07 ribosomal protein L23 (RPL23) 17 1.11 1.99 1.27 2-015H10 Sec61 gamma (SEC61G) 7 -1.01 1.22 1.22 2-026F11 mitochondrial ribosomal protein S18-2 6 1.26 1.84 1.59 BL-004A06 mitochondrial ribosomal protein L19 2 -1.01 1.3 1.22 2-028E11 ribosome-binding protein 1 (RRBP1) 20 1.14 1.54 1.54 Proteolysis 2-012D09 ubiquitin-conjugating enzyme E2G 1 17 -1.14 1.55 1.2 2-031C12 chromosome 20 open reading frame 18 20 -1.02 1.46 1.32 2-006G10 hypothetical protein FLJ21839 2 1.17 1.07 1.51 2-016G11 neural precursor cell expressed developmentally down-regulated 8 (NEDD8) 14 1.05 1.74 1.19 2-006C07 COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis) 7 1.12 1.18 1.33 2-034B08 COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis) 15 -1.34 1.09 1.41 Muscle contraction 2-004B08 actin alpha 1 skeletal muscle (ACTA1) 1 1.01 1.17 1.25 2-022F10 myoglobin (MB) 22 1.76 1.76 1.84 2-023H07 myosin heavy polypeptide 7 cardiac muscle beta (MYH7) 14 -1.04 1.29 1.14 Myogenesis 2-002F04 four and a half LIM domains 1 (FHL1) X -1.25 1.06 -1.15 2-002B02 cysteine and glycine-rich protein 3 (cardiac LIM protein) (CSRP3) 11 -1.2 1.32 1.32 Cell cycle control 2-015H04 cyclin I (CCNI) 4 -1.46 -1.45 -1.2 BL-006D06 PERP, TP53 apoptosis effector 15 1.09 1 1.36 BL-010C02 retinoblastoma binding protein 6 9 -1.31 -1.34 1.06 2-026A06 dynein cytoplasmic heavy polypeptide 1 14 -1.42 -1.02 -1.04 Signal transduction 2-016F07 protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha (PPP2R3A) 3 -1.31 1.41 1.18 2-017B07 basigin (BSG) 19 -1.06 1.27 1.14 Immune response 2-016C06 major histocompatibility complex class IIDP beta 1 (HLA-DPB1) 6 -1.03 1.4 1.41 Oxidative stress response 2-010C03 carboxy terminal LIM domain protein 1 10 1.08 1.01 1.45 2-010B07 glutathione S-transferase pi (GSTP1) 11 -1.01 1.16 1.38 2-016A11 peroxiredoxin 1 (PRDX1) 1 -1.14 1.38 1.25 Other 2-026E07 glutamic-oxaloacetic transaminase 2 mitochondrial (GOT2) 16 -1.06 1.12 1.41 2-033B07 PEST-containing nuclear protein (pcnp) 3 -1.2 1.07 1.5 BL-005E12 adenosine deaminase (ADA) 20 -1.18 1.21 1.12 2-028F01 S-adenosyl homocysteine hydrolase-like 1 (AHCYL1) 1 1.27 1.55 1.29 2-033B12 URB, steroid sensitive gene 1 3 1.45 2.09 2.08 2-035F06 heat shock protein, alpha-crystallin-related, B6 19 -1.25 1.52 1.59 Unknown 2-008F10 unknown sequence from clone RP4-713B5 1 -1.18 -1.06 1.65 2-031C02 unknown sequence from BAC clone RP11-331D5 7 -1.33 -1.15 1.83 2-033F02 PP14397 mRNA 16 -1.07 1.27 1.65 BL-003D02 unknown sequence from clone HRPC837J 17 -1.32 1.1 1.23 2-032C05 unknown sequence from BAC RP11-631N16 12 -1.38 -1.1 1.52 2-022F06 FYVE and coiled-coil domain containing 1 (FYCO1) 3 -1.26 1.13 1.42 2-029F06 hypothetical protein FLJ10815 16 -1.07 1.34 1.32
Table F
Human Muscle Array Averaged expression ratios (FSHD/control) Gene name and biological process Chr pos 2.0 Archive ID Group A Group B Group C Frgm > 21Kb 21Kb < Frgm > 16Kb Frgm = 10Kb Glycolysis 2-035G11 enolase 3 (ENO3) 17 1.92 1.14 1.16 2-001A03 glyceraldehyde-3-phosphate dehydrogenase (GAPD) 12 1.33 -1.01 1 2-023G06 phosphoglycerate mutase 2 (muscle) 7 2.71 1.19 1.12 2-018D10 phosphoglycerate mutase 2 (muscle) 7 1.61 1.06 1.02 2-026D03 triosephosphate isomerase 1 (TPI1) 12 1.63 1.07 1.18 Oxidative phosphorilation 2-022D11 NADH dehydrogenase (ubiquinone) 1 beta subcomplex 7 19 1.8 1.13 1.5 2-002C11 NADH dehydrogenase (ubiquinone) 1 beta subcomplex 3 2 1.27 1.38 1.07 2-022G05 NADH dehydrogenase (ubiquinone) 1 beta subcomplex 9 8 1.1 1.54 -1.07 Transcripts codified by mitochondrial genome 2-041A07 16 S ribosomal RNA 1.24 1.45 -1.46 2-041B04 NADH dehydrogenase subunit 2 1.41 1.21 1.26 2-041B03 NADH dehydrogenase subunit 2 1.33 1.14 1.12 2-041B12 cytochrome oxidase subunit I (COX1) 1.46 1.98 -1.21 Protein biosynthesis 2-018E08 HIGHLY SIMILAR TO ribosomal protein L23a (RPL23A) 17 1.66 -1.29 -1.44 2-024G01 ribosomal protein L13a (RPL13A) 19 1.56 1.24 1.04 BL-001C06 ribosomal protein L4 (RPL4) 15 1.49 -1.41 -1.07 BL-001B10 ribosomal protein S16 (RPS16) 19 1.37 -1.14 1.12 BL-001E11 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 17 1.09 -1.12 -1.26 2-001C11 ribosomal protein L21 (gene or pseudogene) (RPL21) 10 1.58 -1.1 -1.17 2-030G04 mitochondrial ribosomal protein L23 (MRPL23) 1 -1.09 -1.49 -1.32 2-002G04 ribosomal protein L26 (RPL26) 17 -1.37 -1.02 -1.62 2-022B11 ribosomal protein L18 (RPL18) 19 1.26 1.02 -1.12 2-020H07 ribosomal protein L10 (RPL10) X 1.49 1.05 1.06 BL-001A03 ribosomal protein S27 (metallopanstimulin 1) (RPS27) 1 1.22 -1.37 -1.6 2-023H06 HIGHLY SIMILAR TO ornithine decarboxylase antizyme 1 (OAZ1) 19 1.78 1.26 1.19 Proteolysis 2-026C11 proteasome subunit beta type 5 (PSMB5) 14 1.27 1.27 1.2 2-029A02 cathepsin B (CTSB) 8 2.12 1.15 1.6 2-031F08 proteasome subunit alpha type 3 (PSMA3) 14 1.13 1.32 -1.09 Muscle contraction 2-020H03 actinin alpha 2 (ACTN2) 1 1.7 1.05 1.15 2-020F04 creatine kinase muscle (CKM) 19 2.86 -1.01 1.12 2-021E02 FATZ1 or MYOZ1 10 1.79 -1.05 1.15 2-018E09 myosin heavy polypeptide 1skeletal muscle adult (MYH1) 17 1 -1.33 -1.8 2-001B02 myosin heavy polypeptide 2 skeletal muscle adult (MYH2) 17 -1.11 -1.12 -1.36 2-001B08 myosin light chain 2 16 1.71 1.05 1.02 2-036F05 myosin, light polypeptide 7, regulatory 19 2.68 -1.03 1.23 2-018C06 nebulin (NEB) 2 -1.3 1.03 -1.67 2-010B10 titin (TTN) 2 1.14 1.21 -1.18 2-001A05 titin-cap (telethonin) (TCAP) 17 2 -1.22 1.03 2-021C11 skeletal beta-tropomyosin 9 2.02 -1.02 1.27 2-003E06 tropomodulin 4 (muscle) (TMOD4) 1 1.98 -1.03 -1.09 2-001E09 troponin C2 fast (TNNC2) 20 1.4 -1.15 -1.06 2-022B02 troponin I skeletal fast (TNNI2) 11 2.09 1.48 -1.09 2-024D08 troponin T1 skeletal slow 19 2.79 1.1 1.18 2-024F11 troponin T3 skeletal fast (TNNT3) 11 4.13 -1.59 -1.11 Cytoskeleton 2-005F08 ankyrin 1 erythrocytic (ANK1) variant 4 8 1.62 -1.03 1.24 2-020B02 desmin (DES) 2 1.52 -1.05 1.09 Cell cycle control BL-003H11 putative lymphocyte G0/G1 switch gene (G0S2) 1 2.07 -1.15 -1.37 Regulation of transcription BL-003B05 TBP-associated factor 55 kD (TAF7) 5 -1.33 -1.29 -1.43 2-031E08 retinoid X receptor beta 6 1.76 1.96 1.53 2-024D01 calreticulin (CALR) 19 1.13 -1.22 -1.3 2-006H05 NFKBIA 14 1.28 -1.05 -1.03 Signal transduction 2-026E10 ras homolog gene family member C (ARHC) 1 1.97 -1.06 1.42 2-029G10 HIGHLY SIMILAR TO RAB7 member RAS oncogene family 3 1.15 -1.16 -1.41 BL-001A01 RAS p21 protein activator (GTPase activating protein) 1 5 1.17 -1.33 -1.23 2-031H08 calmodulin 2 2 1.64 1.51 1.1 2-033H09 ring finger protein 139 8 2.53 1.11 1.66 Extracellular matrix 2-025E09 SIMILAR TO laminin alpha 4 6 4.21 -1.52 -1.13 Other 2-015C01 aldehyde dehydrogenase 2 mitochondrial (ALDH2) 12 1.04 -1.02 -1.29 2-020G09 clathrin light polypeptide (Lcb) (CLTB) 4 1.65 -1.04 -1.11 2-027D01 sperm associated antigen 7 (SPAG7) 17 1.52 1.14 1.21 2-013E12 heat shock protein 47 member 1 11 1.58 -1.07 1.04 Unknown 2-003E11 cDNA FLJ32423 20 1.21 -1.22 -1.3 2-007E05 unknown sequence from clone 565E6 11 -1.04 -1.5 -1.34 2-020D03 SCIRP10-related protein 1 5.17 -1.58 -1.12 2-031F07 chromosome 10 open reading frame 70 10 2.1 1.33 1.08 2-032D02 unknown sequence from clone CTD-3162L10 19 1.42 -1.42 1.16 2-033B08 unknown sequence from clone RP11-128A17 15 1.15 -1.69 -1.34 2-033B10 hypothetical protein FLJ22965 X 1.64 1.8 1.09 BL-003C05 unknown sequence from 12 BAC RP11-225E24 12 1.02 -1.47 -1.19 BL-006F03 chromosome 10 open reading frame 32 10 -1.04 -1.4 -1.26 2-013A06 PDZ and LIM domain 5 4 1.08 1.12 -1.45 BL-010H03 unknown sequence from BAC clone RP11-181K12 4 1.03 -1.49 -1.54 2-033H08 hypothetical protein DKFZp434L142 4 -1.02 -1.47 -1.38 2-031F11 cDNA FLJ39585 8 -1.4 -1.03 -1.49 BL-009D09 clone RP11-17L7 9 1.15 -1.9 -1.4 2-015H06 similar to RIKEN cDNA 1110030K22 11 1.99 1.04 1.09
Table G
Human Muscle Array Expression ratios (FSHD/control) Averaged expression ratios (FSHD/control) Gene name and biological process 2.0 Archive ID Group A Group B Group C Group A Group B Group C 21Kb < Frgm > 3-26 kb 4-23 Kb 6-21 Kb 7-19 Kb 8-16 Kb 9-10 Kb 10-10 Kb 11-10 Kb Frgm > 21Kb 16Kb Frgm = 10Kb Glycolysis 2-035G11 enolase 3, (beta, muscle) (ENO3) 1.7 2.47 1.6 NA 1.14 NA -1.14 1.45 1.92 1.14 1.16 2-001A03 glyceraldehyde-3-phosphate dehydrogenase (GAPD) 1.31 1.38 1.29 1.07 -1.1 -1.03 1.1 -1.07 1.33 -1.01 1 2-023G06 phosphoglycerate mutase 2 (muscle) 3.12 NA 2.29 1.43 -1.05 1.13 1.01 1.22 2.71 1.19 1.12 2-026D03 triosephosphate isomerase 1 (TPI1) 1.66 NA 1.6 1.12 1.03 1.3 1.21 1.04 1.63 1.07 1.18 Transcripts codified by mitochondrial genome 2-041C03 ATP synthase F0 subunit 6 (ATP6) 1.95 1.84 1.15 1.81 NA 1.15 1.86 1.52 1.65 1.81 1.51 2-041D09 cytochrome b (cytb) 2.21 2.2 1.46 NA 1.39 1.62 1.76 1.63 1.96 1.39 1.67 2-041C02 cytochrome oxidase subunit II (COX2) 2.88 2.22 1.13 NA 2.06 1.94 2.21 1.89 2.08 2.06 2.01 2-041B02 NADH dehydrogenase subunit 1 1.39 1.47 1.41 NA 1.26 1.54 1.85 1.35 1.43 1.26 1.58 2-041B04 NADH dehydrogenase subunit 2 1.56 1.38 1.3 1.33 1.09 1.12 1.41 1.25 1.41 1.21 1.26 2-041C12 NADH dehydrogenase subunit 4 1.83 1.93 1.15 1.4 NA 1.33 2.03 1.38 1.64 1.4 1.58 Muscle contraction 2-023A02 creatine kinase, muscle (CKM) 2.13 1.8 1.84 -1.23 -1.1 1.13 1.44 -1.01 1.92 -1.16 1.19 2-021E02 FATZ 1 or MYOZ 1 1.46 2.05 1.87 -1.18 1.06 1.3 -1 NA 1.79 -1.05 1.15 2-022F10 myoglobin (MB) NA 1.9 1.62 1.46 2.06 2.08 1.8 1.65 1.76 1.76 1.84 2-018E09 myosin, heavy polypeptide 1, (MYH1) -2.32 1.62 -1.04 -2.88 1.15 -2.13 -1.41 -2.04 1 -1.33 -1.8 2-001B02 myosin, heavy polypeptide 2, skeletal muscle, adult (MYH2) -1.19 -1 -1.15 NA -1.12 -1.34 -1.33 -1.41 -1.11 -1.12 -1.36 2-023H07 myosin, heavy polypeptide 7, cardiac muscle, beta (MYH7) 1.08 NA -1.18 1.28 1.31 1.08 1.05 1.27 -1.04 1.29 1.14 2-023E04 myosin, light polypeptide 3, alkali; (MYL3) 2 NA 1.82 1.12 NA 1.91 1.46 1.85 1.91 1.12 1.74 2-001B08 myosin light chain 2 (HUMMLC2B) 2.13 1.81 1.19 -1.28 1.32 -1.02 -1.09 1.16 1.71 1.05 1.02 2-010A08 myosin, light polypeptide 3, alkali; ventricular, skeletal, slow NA 1.3 1.32 1.19 -1.02 1.32 1.23 1.14 1.31 1.09 1.23 2-001E09 troponin C2, fast (TNNC2) 1.16 1.75 1.29 -1.49 1.07 -1.02 -1.11 -1.04 1.4 -1.15 -1.06 2-022B02 troponin I, skeletal, fast (TNNI2) 1.95 2.7 1.64 NA 1.48 -1.29 -1.1 1.07 2.09 1.48 -1.09 2-021A01 troponin I, skeletal, slow (TNNI1) NA 1.31 1.37 -1 -1.05 1.78 1.23 1.66 1.34 -1.02 1.55 2-023F09 troponin T1, skeletal, slow (TNNT1) 3.07 3.2 2.31 1.05 NA 1.24 1.08 1.41 2.86 1.05 1.24 2-022C04 troponin T3, skeletal, fast (TNNT3) NA 7.53 3.86 -2.12 NA -1.24 1.18 1.13 5.69 -2.12 1.04 Regulation of transcription 2-024D01 calreticulin (CALR) NA NA 1.13 -1.14 -1.3 -1.36 -1.16 -1.4 1.13 -1.22 -1.3 2-013B01 peroxisome proliferative activated receptor, alpha (PPARA) 1.87 1.7 1.06 1.38 2.21 1.56 1.31 1.57 1.55 1.79 1.48 Extracellular matrix 2-025E09 laminin, alpha 4 (LAMA4) 4.51 4.76 3.36 -1.52 NA -1.09 -1.18 -1.13 4.21 -1.52 -1.13
Table H
Human Muscle Array Averaged expression ratios (FSHD/control) Gene name and biological process 2.0 Archive ID Group A Group B Group C Group >50 Frgm > 21Kb 21Kb > Frgm > 16Kb Frgm = 10Kb Frgm > 21Kb Muscle contraction 2-001H03 actinin, alpha 2 -1.05 1.02 -1.02 1.1 2-010G04 sarcomeric mitochondrial creatine kinase -1.11 1.27 1.01 1.05 2-021F01 ZASP1 -1.93 1.08 -1.04 -1.15 2-021E02 myozenin 1 or FATZ1 1.79 -1.05 1.15 -1.06 2-016A02 myosin binding protein C, slow type 1.04 -1.89 1.26 -1.37 2-001G08 myosin, light polypeptide 1, alkali; skeletal, fast -1.19 1.55 -1.79 -1.13 2-010B01 upregulated during skeletal muscle growth 5 NA 1.18 -1.35 1.02 2-023G04 myosin, heavy polypeptide 7, cardiac muscle, beta 1.51 1 1.37 -1.55 2-023E04 myosin, light polypeptide 3, alkali; ventricular, skeletal, slow (MYL3) 1.91 1.12 1.74 -1.19 2-029C02 myocyte enhancer factor 2C (MEF2C) -1.39 -1.12 -1.22 1.08 2-018E09 myosin, heavy polypeptide 1, skeletal muscle, adult (MYH1) -1.16 -1.33 -1.8 -1.97 2-018F08 nebulin (NEB) -1.11 -1.12 -1.50 1.03 2-001C02 titin (TTN) -1.27 -1.01 -1.68 -1.7 2-001A05 titin-cap (telethonin) (TCAP) 2 -1.22 1.03 -1.65 2-003E06 tropomodulin 4 (muscle) (TMOD4) 1.98 -1.03 -1.09 -1.05 2-006D06 syntrophin, alpha (dystrophin-associated protein A1, 59kD, acidic component) NA -1.01 1.1 -1.03 2-002G10 triadin (TRDN) 1.09 1.4 -1.23 -1.12 2-017H01 troponin C2, fast (TNNC2) 1 1.07 -1.05 1.18 2-021E04 troponin I, skeletal, fast (TNNI2) 2.75 -1.75 -1.05 -2.01 2-024C08 troponin T3, skeletal, fast (TNNT3) 4.36 -1.92 -1.07 -2.05 2-023F09 troponin T1, skeletal, slow 2.86 1.05 1.24 -1.7 Apoptosis 2-026B06 BCL2-associated athanogene NA 1.29 1.16 -1.08 2-017H03 HIGHLY SIMILAR TO chaperone, ABC1 activity of bc1 complex like (S. pombe) (CABC1) 1.29 1.97 1.68 -1.3 2-021C01 heat shock 27kDa protein 1 1.21 1.22 1.1 -1.11 Other 2-006H05 NFKBIA 1.28 -1.05 -1.03 -1.16 2-005G02 NUB1 (NUB1) mRNA -1.09 1.21 -1.1 1.08 2-021C01 heat shock protein HSP27 1.21 1.22 1.1 -1.1 2-018D10 phosphoglycerate mutase 2 (muscle) 1.61 1.06 1.02 1.03 2-002E06 microsomal glutathione S-transferase 3 (MGST3) 1.45 1.41 1.05 1.07 2-003G04 microsomal glutathione S-transferase 2 (MGST2) 1.1 1.24 1.1 1.05 2-017B07 basigin (BSG) -1.06 1.27 1.14 1.06 2-015C10 annexin A2 (ANXA2) 1.48 -1.01 1 1.06 2-002E04 sarcolipin (SLN) -1.04 1.36 1.09 1.08 2-004G09 unknown sequence from clone CTC-467M3 NA -1.08 -1.12 1.01