Supplementary Table II A. List of Up-Regulated Genes

Supplementary Table II A. List of Up-regulated Genes Demonstrating Significant DE not Included in a Priori pathway lists* Gene Gene Name AffyID Fold- p-value GO Pathway Symbol Change SRI sorcin 208921_s_at 1.48 0.000004 Signal transduction, calcuim ion binding PSMB2 proteasome (prosome, macropain) subunit, beta type, 2 200039_s_at 1.34 0.000010 Macromolecule Catabolism GZMB granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated 210164_at 2.33 0.000015 Programmed cell death, serine esterase 1) endopeptidase activity PPA1 pyrophosphatase (inorganic) 1 217848_s_at 1.86 0.000048 Hydrolase activity, phosphorus metabolism PSMA5 proteasome (prosome, macropain) subunit, alpha type, 5 201274_at 1.39 0.000049 Macromolecule Catabolism HSD11B1 hydroxysteroid (11-beta) dehydrogenase 1 205404_at 3.49 0.000052 Lipid metabolism, hormone metabolism GGTLA1 gamma-glutamyltransferase-like activity 1 205582_s_at 3.90 0.000065 Transferase activity, transferring amino acyl groups AKAP2 /// A kinase (PRKA) anchor protein 2 /// PALM2-AKAP2 protein 202760_s_at 1.58 0.000082 Kinase activity, cellular PALM2- morphogenesis AKAP2 NDUFV2 NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa 202941_at 1.34 0.000092 Electron transport, NADH dehydrogenase activity ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 209765_at 1.77 0.000096 Protein metabolism, endopeptidase activity GAPDH glyceraldehyde-3-phosphate dehydrogenase 212581_x_at 1.34 0.000120 Primary metabolism, carbohydrate metabolism ICAM1 intercellular adhesion molecule 1 (CD54), human rhinovirus 202638_s_at 1.50 0.000145 Cell-cell adhesion, transmembrane receptor receptor activity PSMB5 proteasome (prosome, macropain) subunit, beta type, 5 208799_at 1.34 0.000145 Macromolecule Catabolism KIF20A kinesin family member 20A 218755_at 4.62 0.000152 Establishment of cellular localization ST3GAL5 ST3 beta-galactoside alpha-2,3-sialyltransferase 5 203217_s_at 1.35 0.000152 Lipid metabolism, silayltransferase activity PFKP phosphofructokinase, platelet 201037_at 1.52 0.000167 Primary metabolism, carbohydrate metabolism GOLPH2 golgi phosphoprotein 2 217771_at 3.13 0.000200 Cellular response to viral infection TPI1 triosephosphate isomerase 1 213011_s_at 1.32 0.000211 Lipid metabolism MTHFD2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase (NADP+ 201761_at 1.42 0.000226 Heterocycle metabolism dependent) 2 TYMS thymidylate synthetase 202589_at 1.75 0.000226 DNA repair PSMD12 proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 202352_s_at 1.35 0.000231 Macromolecule Catabolism EBNA1BP EBNA1 binding protein 2 201323_at 1.43 0.000244 Cell organization and biogenesis 2 SC4MOL sterol-C4-methyl oxidase-like 209146_at 1.39 0.000247 Lipid metabolism, monooxigenase activity LAMP3 lysosomal-associated membrane protein 3 205569_at 1.66 0.000283 Cell proliferation SLC25A17 solute carrier family 25 (mitochondrial carrier; peroxisomal membrane 214210_at 1.79 0.000349 Intracellular transport, protein, 34kDa), member 17 establishment of localization PSMA2 proteasome (prosome, macropain) subunit, alpha type, 2 201317_s_at 1.41 0.000395 Macromolecule Catabolism CDC40 cell division cycle 40 homolog (yeast) 203376_at 1.34 0.000400 Cell division MT2A metallothionein 2A 212185_x_at 1.72 0.000417 Ion homeostasis, metal ion binding PHLDA2 pleckstrin homology-like domain, family A, member 2 209803_s_at 1.84 0.000566 Programmed cell death ALAS1 aminolevulinate, delta-, synthase 1 205633_s_at 1.60 0.000591 Heterocycle metabolism, transferase activity CENPA centromere protein A, 17kDa 204962_s_at 1.76 0.000638 DNA binding, cell organization and biogenesis VRK2 vaccinia related kinase 2 205126_at 1.45 0.000693 Macromolecule metabolism, kinase activity SLC39A8 solute carrier family 39 (zinc transporter), member 8 209267_s_at 1.68 0.000802 Ion transport MT1X metallothionein 1X 204326_x_at 1.77 0.000952 Electron transport, metal ion binding * Genes in bold text have associated functions that could be assigned to an a-priori pathway ** (VLP-Media) expression levels as defined in the Materials and Methods Section

Supplementary Table II B. List of Down-Regulated Genes Demonstrating Significant DE not Included in a Priori pathway lists Gene Gene Name AffyID Fold- p-value GO Pathway Symbol Change CD9 CD9 antigen (p24) 201005_at -1.82 0.0000001 Cell maturation, cell motility CD99 CD99 antigen 201029_s_at -1.30 0.0000016 T-cell, cell adhesion SDS serine dehydratase 205695_at -2.51 0.0000094 Ammonia-lyase activity SORL1 sortilin-related receptor, L(DLR class) A repeats-containing 203509_at -1.71 0.0000119 Transmembrane receptor activity, lipid transport CYP27A1 cytochrome P450, family 27, subfamily A, polypeptide 1 203979_at -2.14 0.0000323 Monooxygenase activity, steroid hydorxylase activity HOMER3 homer homolog 3 (Drosophila) 204647_at -1.99 0.0000557 Signal transduction PDK4 pyruvate dehydrogenase kinase, isoenzyme 4 205960_at -2.80 0.0000815 Primary metabolism, kinase activity DFNA5 deafness, autosomal dominant 5 203695_s_at -1.82 0.0000886 Sensory perception of mechanical stimulus DGCR2 DiGeorge syndrome critical region gene 2 214198_s_at -1.34 0.0001009 Organ morphogenesis ISYNA1 myo-inositol 1-phosphate synthase A1 222240_s_at -1.36 0.0001577 Carbohydrate metabolism APOE apolipoprotein E 203382_s_at -2.95 0.0001833 low-density lipoprotein receptor binding SIGIRR single immunoglobulin and toll-interleukin 1 receptor (TIR) 52940_at -1.52 0.0002041 Immune response, negative domain regulation of signal transduction P8 p8 protein (candidate of metastasis 1) 209230_s_at -2.44 0.0002315 Regulation of cell size, programmed cell death DNASE2 deoxyribonuclease II, lysosomal 209831_x_at -1.35 0.0002354 Nuclease activity, programmed cell death ALDH3A2 aldehyde dehydrogenase 3 family, member A2 202054_s_at -1.48 0.0002564 Aldehyde metabolism, oxidoreductase activity HS3ST2 heparan sulfate (glucosamine) 3-O-sulfotransferase 2 219697_at -2.64 0.0002601 Sulfotransferase activity VAT1 vesicle amine transport protein 1 homolog (T californica) 208626_s_at -1.30 0.0002689 Cellular morphogenesis, regulation of cell size SNCA synuclein, alpha (non A4 component of amyloid precursor) 204466_s_at -1.58 0.0002863 Programmed cell death, nervous system development RARRES1 retinoic acid receptor responder (tazarotene induced) 1 221872_at -2.32 0.0004026 Cell proliferation, negative regulation of cellular process GLTSCR1 glioma tumor suppressor candidate region gene 1 219445_at -1.58 0.0004039 Cell adhesion GCHFR GTP cyclohydrolase I feedback regulator 204867_at -1.75 0.0004079 Cell-cell signaling, neurotransmitter metabolism KCNJ14 potassium inwardly-rectifying channel, subfamily J, member 14 220776_at -1.89 0.0004521 Ion channel activity DAB2 Disabled homolog 2, mitogen-responsive phosphoprotein 201278_at -1.52 0.0004964 Cell proliferation (Drosophila) ADFP adipose differentiation-related protein 209122_at -1.60 0.0005105 Membrane, lipoprotein CTSD cathepsin D (lysosomal aspartyl peptidase) 200766_at -1.54 0.0005439 Endopeptidase activity ZNF238 zinc finger protein 238 212774_at -1.54 0.0006882 Transcription factor activity, metal ion binding DNAJB2 DnaJ (Hsp40) homolog, subfamily B, member 2 202500_at -1.50 0.0006951 Macromolecule metabolism DHRS10 dehydrogenase/reductase (SDR family) member 10 219113_x_at -1.51 0.0008463 Oxidoreductase activity ACP5 acid phosphatase 5, tartrate resistant 204638_at -1.39 0.0008614 Hydrolase activity, acting on ester bonds GPR175 G protein-coupled receptor 175 218855_at -1.51 0.0009593 G-protein coupled receptor activity * Genes in bold text have associated functions that could be assigned to an a-priori pathway ** (VLP-Media) expression levels as defined in the Materials and Methods Section