Genes transactivated by hepatitis C virus core protein, a microarray assay

Table 1 Up-regulated genes by HCV core.

Accession numbers	Protein	Cy5/Cy3
NM_005657	Tumor protein p53 binding protein 1, TP53BP1	2.004
D50683	TGF-betaIIR alpha	2.072
NM_006595	Apoptosis inhibitor 5, API5	2.199
NM_000612	Insulin-like growth factor 2, IGF2	2.232
NM_002530	Neurotrophic tyrosine kinase, receptor	2.233
NM_000760	Colony stimulating factor 3 receptor, CSF3R	2.253
NM_014350	TNF-induced protein, GG2-1	2.358
NM_006290	Tumor necrosis factor, alpha-induced protein 3, TNFAIP3	2.359
NM_003151	Signal transducer and activator of transcription 4, STAT4	2.390
U07139	Voltage-gated calcium channel beta subunit	2.423
NM_000014	Alpha-2-macroglobulin, A2M	2.526
NM_012112	Chromosome 20 open reading frame 1, C20orf1	2.689
NM_002736	Protein kinase, cAMP- dependent, regulatory	2.710
NM_014575	Schwannomin interacting protein 1, SCHIP1	2.737
U47077	DNA-dependent protein kinase catalytic subunit, DNA-PKcs	2.787
AF352051	Proliferation potential-related protein	2.827
NM_003998	Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1, p105, NF-kB1	3.005
NM_004728	DEAD/H box polypeptide 21	3.149
NM_005100	A kinase anchor protein 12, AKAP12	3.897
NM_005171	Activating transcription factor 1, ATF1	4.142
BC008959	Histocompatibility 13	4.760
NM_014863	B cell RAG associated protein, BRAG	5.769
NM_002291	Laminin, beta 1, LAMB1	10.334

Table 2 Down-regulated genes by HCV core.

Accession numbers	Protein	Cy5/Cy3
NM_000535	PMS2 postmeiotic segregation increased 2	0.122
NM_012096	Adaptor protein containing pH domain, PTB domain and leucine zipper motif, APPL	0.386
NM_003844	Tumor necrosis factor receptor superfamily, member 10a	0.388
NM_001226	Caspase 6, apoptosis-related cysteine protease	0.400
NM_001229	Caspase 9, apoptosis-related cysteine protease	0.429
NM_002287	Leukocyte-associated Ig-like receptor 1	0.440
AF090693	Apoptosis-related RNA binding protein	0.462
NM_021020	Leucine zipper, putative tumor suppressor 1 LZTS1	0.464
NM_000062	Serine or cysteine proteinase inhibitor	0.471
NM_000575	Interleukin 1, alpha	0.472
AF016266	TRAIL receptor 2	0.477
NM_003796	RNA polymerase II subunit 5 RPB5-mediating protein, RMP	0.485
NM_000629	Interferon alpha, beta and omega receptor 1,IFNAR1	0.494

Table 3 Up-regulated genes by HCTP4 protein.

Accession numbers	Protein	Cy5/Cy3
NM_002599	Phosphodiesterase 2A, cGMP-stimulated (PDE2A)	2.011
NM_053274	FKBP-associated protein (FAP48), transcript variant 1	2.014
NM_012319	LIV-1 protein, estrogen regulated (LIV-1)	2.017
NM_007047	Butyrophilin,subfamily 3, member A2 (BTN3A2)	2.030
NM_021950	Membrane-spanning 4-domains, subfamily A, member 1 (MS4A1)	2.033
NM_000817	Glutamate decarboxylase 1 (GAD1)	2.048
NM_033625	Ribosomal protein L34 (RPL34)	2.055
NM_006526	Zinc finger protein 217 (ZNF217)	2.058
NM_112219	Esterase D	2.068
NM_000386	Bleomycin hydrolase (BLMH)	2.079
NM_006330	Lysophospholipase 1 (LYPLA1)	2.088
D21262	KIAA0035 gene	2.089
NM_003796	RPB5-mediating protein (RMP)	2.091
NM_004904	cAMP response element-binding protein (CRE-BPa)	2.096
AF012086	Ran binding protein 2 (RanBP2alpha)	2.118
NM_005836	Translational inhibitor protein p14.5 (UK114)	2.126
NM_003998	Heat shock 70 ku protein 8 (HSPA8)	2.138
NM_000816	Gamma-aminobutyric acid (GABA)A receptor, gamma 2 (GABRG2)	2.174
NM_003129	Squalene epoxidase (SQLE)	2.174
NM_022171	T-cell leukemia translocation altered gene (TCTA)	2.211
NM_006644	Heat shock 105 ku (HSP105B)	2.256
AF070674	Inhibitor of apoptosis protein-1 (MIHC)	2.281
NM_001892	Casein kinase 1, alpha 1 (CSNK1A1)	2.285
NM_001539	Heat shock protein, DNAJ-like 2 (HSJ2)	2.303
NM_013943	Chloride intracellular channel 4 (CLIC4)	2.325
NM_006407	Vitamin A responsive; cytoskeleton related (JVVA)	2.370
NM_014637	T-cell receptor rearranged beta chain gene V-region (V-D-J)V-beta-AT	2.395
M11952	Nuclear receptor subfamily 3, group C, member 1 (NR3C1)	2.396
NM_007268	Ig superfamily protein (Z391G)	2.445
NM_021129	Pyrophosphatase (inorganic) (PP), nuclear gene encoding mitochondrial protein	2.498
NM_002731	Protein kinase, cAMP-dependent, catalytic, beta (PRKACB)	2.525
D85606	Gene for cholecystokinin type-A receptor	2.635
NM_024824	Hypothetical protein FLJ11806 (FLJ11806)	2.730
AF072928	Myotubularin related protein 6	2.802

Table 4 Down-regulated genes by HCV core.

Accession numbers	Protein	Cy5/Cy3
NM_001961	Eukaryotic translation elongation factor 2 (EEF2)	0.040
NM_002313	Actin binding LIM protein 1 (LIM), transcript variant ABLIM-1	0.214
NM_014680	KIAA0100 gene product (KIAA0100)	0.234
NM_003682	MAP-kinase activating death domain (MADD)	0.259
NM_001226	Prosaposin	0.266
NM_004728	DEAD/H box polypeptide 21 (DDX21)	0.313
NM_013975	Ligase III, DNA, ATP-dependent (LIG3)	0.317
NM_014889	Metalloprotease 1 (MP1)	0.347
NM_005770	Small EDRK-rich factor 2 (SERF2)	0.348
NM_005167	Ras homolog gene family, member C (ARHC)	0.368
NM_000208	Insulin receptor (INSR)	0.369
NM_003330	Thioredoxin reductase 1 (TXNRD1)	0.373
NM_005243	Ewing sarcoma breakpoint region 1 (EWSR1)	0.396
NM_016250	N-myc downstream-regulated gene 2 (NDRG2)	0.404
NM_001250	Tumor necrosis factor receptor superfamily, member 5 (TNFRSF5)	0.406
NM_003313	Tissue specific transplantation antigen P35B (TSTA3)	0.416
NM_004127	G protein pathway suppressor 1 (GPS1)	0.416
NM_002708	Protein phosphatase 1, catalytic subunit, alpha isoform (PPP1CA)	0.431
NM_001777	CD47 antigen (Rh-related antigen, integrin-associated signal transducer	0.444
NM_002199	Interferon regulatory factor 2 (IRF2)	0.454
NM_002087	Granulin (GRN)	0.469
NM_000660	Transforming growth factor, beta 1 (TGFB1)	0.475
NM_054012	Argininosuccinate synthetase (ASS)	0.478
NM_002084	Glutathione peroxidase 3 (GPX3)	0.493