Additional file 4

Additional file 4. Fold-changes (FC) and functional categories of 57 selected genes (58 probes) modulated by HCV in all replicon clones #

Gene_Name Gene_Symbol secreted phosphoprotein 1 (osteopontin) SPP1 leprecan-like 1 LEPREL1 alpha-2-HS-glycoprotein AHSG coagulation factor C homolog, cochlin (Limulus polyphemus) COCH histone 2, H2aa|histone 2, H2ac HIST2H2AA|HIST2H2AC histone 2, H2aa HIST2H2AA histone 1, H1c HIST1H1C histone 1, H2ab HIST1H2AB histone 3, H2a HIST3H2A interferon, alpha-inducible protein (clone IFI-15K) G1P2 nucleolar protein family A, member 3 NOLA3 mitochondrial ribosomal protein L18 MRPL18 mitochondrial ribosomal protein L13 MRPL13 ribosomal protein L15 RPL15 Parkinson disease (autosomal recessive, early onset) 7 PARK7 SRY (sex determining region Y)-box 9 SOX9 heterogeneous nuclear ribonucleoprotein D-like HNRPDL eukaryotic translation initiation factor 3, subunit 6 interacting proteinEIF3S6IP staufen, RNA binding protein, homolog 2 (Drosophila) STAU2 carbamoyl-phosphate synthetase 2 CAD pseudouridylate synthase-like 1 PUSL1 N.A. LOC392347 chromatin modifying protein 4A CHMP4A lectin, mannose-binding 2-like LMAN2L RALBP1 associated Eps domain containing 1 REPS1 tubulin, beta 2A TUBB2A mal, T-cell differentiation protein 2 MAL2 mitochondrial GTPase 1 homolog (S. cerevisiae) MTG1 ornithine aminotransferase (gyrate atrophy) OAT phosphoglycerate mutase 1 (brain) PGAM1 centromere protein E, 312kDa CENPE metastasis suppressor 1 MTSS1 coiled-coil domain containing 80 URB OAF homolog (Drosophila) OAF ELOVL family member 6, elongation of long chain fatty acids ELOVL6 DNA-damage-inducible transcript 3 DDIT3 WW domain containing E3 ubiquitin protein ligase 1 WWP1 UDP-N-acteylglucosamine pyrophosphorylase 1 UAP1 serpin peptidase inhibitor, clade C (antithrombin), member 1 SERPINC1 proprotein convertase subtilisin/kexin type 5 PCSK5 guanine nucleotide binding protein (G protein), beta polypeptide 1 GNB1 guanine nucleotide binding protein (G protein), gamma 5 GNG5 calmodulin binding transcription activator 1 CAMTA1 CD59 antigen p18-20 CD59 galanin GAL ATP-binding cassette-ATG9 autophagy related 9 homolog A ABCB6-ATG9A phosphatidylinositol transfer protein, membrane-associated 1 PITPNM1 ring finger protein 190 RNF190 optineurin OPTN transmembrane protein 63A TMEM63A COMM domain containing 8 COMMD8 transmembrane protein 70 TMEM70 cell division cycle associated 7 CDCA7 eukaryotic translation initiation factor 4E nuclear import factor 1 EIF4ENIF1 erythrocyte membrane protein band 4.1-like 1 EPB41L1 leucine rich repeat and coiled-coil domain containing 1 LRRCC1

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Primary_Gene_ID * 6696 55214 197 1690 8338 8337 3006 8335 92815 9636 55505 29074 28998 6138 11315 6662 9987 51386 27067 790 126789 392347 29082 81562 85021 7280 114569 92170 4942 5223 1062 9788 151887 220323 79071 1649 11059 6675 462 5125 2782 2787 23261 966 51083 ¶ 10058-79065 9600 162333 10133 9725 54951 54968 83879 56478 2036 85444

ProbeID 186825 ▲ 121792-134755 186803 189694 149647 139881-150267▲ 206232 162382 209319 133610 189298 197989 108144 211819 136848 201106 158620 147314 151128 113678 142230 189484 190678 184532 147893 194068 194621 121062 196523 187172 165425 188654 111796 121408 216339 163509 191676 120981 107675 178884 206443 178569 164871 162611 167511 209528 128232 197739 129441 184048 127990 173256 207416 166561 122347 200352

Genes showing a FC with p ≤ 0.05 in all three datasets (1, 2 and 3) are reported in bold; FC of the other genes showed p ≤ 0.05 in dataset 1 and 3 N.A.: not assigned Two different probes identify the same gene. FC corresponding to the first probe are shown. ¶ Two different genes are identified by the same probe ▲

FC (dataset 1) 3.93 2.93 -2.77 -1.44 3.33 3.40 3.11 2.14 1.37 1.46 1.62 1.31 -1.25 -1.40 1.65 1.34 -1.60 -1.25 -2.00 1.32 1.70 -2.00 1.58 1.34 1.45 2.05 -1.60 -1.60 -1.30 -1.30 1.91 -2.50 6.25 -2.50 -2.00 1.96 -1.60 -2.50 -2.50 5.76 1.41 1.41 1.57 1.83 -2.50 1.86 1.77 1.44 1.42 -1.40 -1.60 -1.25 -1.60 -1.60 -2.00 -3.30

p-value 0.04424 0.00190 0.01289 0.04389 0.00084 0.00451 0.02024 0.02288 0.02435 0.03502 0.00016 0.04743 0.04667 0.03461 0.00256 0.01193 0.00369 0.04855 0.02005 0.03305 0.03460 0.00645 0.00412 0.02258 0.01041 0.02892 0.00297 0.00042 0.04518 0.00741 0.01026 0.02671 0.00400 0.01014 0.00836 0.02985 0.02962 0.04612 0.04040 0.00085 0.03384 0.03747 0.02239 0.01405 0.01756 0.01649 0.00536 0.03907 0.03900 0.03327 0.04959 0.03320 0.03533 0.00258 0.00480 0.01610

FC (dataset 2) 20.31 2.27 -1.80 -1.37 2.23 2.33 2.23 1.42 1.36 3.69 1.57 1.22 -1.40 -1.10 1.35 1.28 -1.25 -1.25 -2.50 1.61 1.75 -1.25 1.93 1.14 1.36 1.17 -1.60 -1.60 -1.60 -1.25 1.42 -2.00 6.82 -1.25 -2.50 2.57 -1.40 -2.50 -5.00 3.67 1.42 1.32 1.29 1.83 -3.30 2.56 1.19 1.42 1.55 -1.60 -1.60 -1.10 -1.40 -1.25 -2.00 -1.42

p-value 0.00081 0.01008 0.03191 0.01590 0.00154 0.01219 0.00682 0.11108 0.04659 0.00014 0.01657 0.15189 0.02570 0.47122 0.02759 0.03671 0.03770 0.05087 0.00713 0.03762 0.01421 0.07531 0.01251 0.23656 0.01581 0.16997 0.00059 0.00036 0.00401 0.02002 0.05624 0.06249 0.00428 0.21529 0.00104 0.00182 0.07106 0.04547 0.00556 0.00367 0.03691 0.11380 0.15521 0.00271 0.00823 0.01220 0.12377 0.04236 0.02416 0.00117 0.05728 0.33313 0.10852 0.01037 0.07714 0.34595

FC (dataset 3) 9.02 2.51 -1.64 -1.56 3.01 2.71 2.36 1.78 1.59 2.40 1.53 1.39 -1.40 -1.60 1.53 1.48 -1.25 -1.25 -2.00 1.76 1.74 -1.42 1.90 1.43 1.35 1.24 -1.40 -1.60 -2.00 -1.30 1.44 -2.50 4.37 -2.00 -2.00 2.07 -1.42 -2.50 -3.30 3.27 1.69 1.50 1.43 1.48 -3.30 2.74 1.61 1.50 1.41 -1.40 -1.40 -1.60 -1.60 -1.60 -2.00 -2.50

p-value 0.00471 0.00773 0.01521 0.00068 0.00098 0.00105 0.01426 0.03605 0.00715 0.00317 0.02152 0.02632 0.01744 0.04747 0.00272 0.00487 0.00145 0.03227 0.00243 0.01649 0.00984 0.00752 0.01692 0.03010 0.00207 0.01343 0.00664 0.00498 0.00049 0.01724 0.01774 0.00163 0.00869 0.02764 0.00426 0.00474 0.00621 0.01566 0.00258 0.00664 0.00407 0.04230 0.04496 0.04245 0.00004 0.00516 0.01931 0.00244 0.04741 0.00187 0.02605 0.04281 0.01646 0.00966 0.04108 0.04805

Molecular Function|Biological Process Extracellular matrix Extracellular matrix glycoprotein Extracellular matrix glycoprotein Extracellular matrix|Cell adhesion molecule Nucleic acid binding|Histone Nucleic acid binding|Histone Nucleic acid binding|Histone Nucleic acid binding|Histone Nucleic acid binding|Histone Nucleic acid binding|Ribosomal protein Nucleic acid binding|Ribosomal protein Nucleic acid binding|Ribosomal protein Nucleic acid binding|Ribosomal protein Nucleic acid binding|Ribosomal protein Nucleic acid binding Nucleic acid binding|Transcription factor Nucleic acid binding|Ribonucleoprotein Nucleic acid binding|Translation initiation factor Nucleic acid binding Nucleoside, nucleotide and nucleic acid metabolism|Pyrimidine metabolism Nucleoside, nucleotide and nucleic acid metabolism|tRNA metabolism Nucleoside, nucleotide and nucleic acid metabolism|Purine metabolism Intracellular protein traffic Intracellular protein traffic|Protein targeting Intracellular protein traffic|Endocytosis Intracellular protein traffic|Chromosome segregation Intracellular protein traffic|General vesicle transport Intracellular protein traffic Amino acid metabolism Carbohydrate metabolism|Glycolysis Cytoskeletal protein|Microtubule binding motor protein Cytoskeletal protein|Actin binding cytoskeletal protein Developmental processes Developmental processes|Neurogenesis Lipid fatty acid and steroid metabolism Oxidative stress Protein metabolism and modification|Proteolysis Protein metabolism and modification|Protein glycosylation Protein metabolism and modification|Proteolysis Signal transducrtion|Cell surface receptor mediated signal transduction Signal transducrtion|Cell surface receptor mediated signal transduction Signal transducrtion|Cell surface receptor mediated signal transduction Signal transduction|Calcium mediated signaling Signaling molecule|Immunity and defense Signaling molecule|Peptide hormone/Muscle contraction Transport|Extracellular transport and import unclassified unclassified unclassified unclassified unclassified unclassified unclassified unclassified unclassified unclassified