Gene expression analysis of primary normal human hepatocytes infected with human hepatitis B virus

Table 1 Forty-five differentially down-regulated genes obtained and categorized by their function

Categoty	UniGene	Gene nam	Symbol	Locus	Function	Control/HBV infection	P-value
Transcription/ RNA Pol II	Hs.442675	Thyroid hormone receptor interactor 8	TRIP8	10	Transcription co-activator of Pol II promoter	3.469	0.030
Transcription	Hs.57475	Sex comb on midleg homolog 1	SCMH1	1p34	Pol II transcription	3.315	0.019
Transcription	Hs.119014	Zinc finger protein 175	ZNF175	19q13.4	C2H2 zinc-finger protein 175	2.942	0.017
Transcription/ RNA Pol II	Hs.437905	Spi-B transcription factor (Spi-1/PU.1 related)	SPIB	19q13.3-q13.4	RNA polymerase II transcription factor	2.743	0.017
Transcription/ RNA Pol II	Hs.148427	LIM homeobox protein 3	LHX3	9q34.3	RNA Pol 2 transcription factor and activate pituitary hormone genes	2.492	0.006
Signal	Hs.17154	Dual-specificity tyrosine-(Y)- phosphorylation regulated kinase 4	DYRK4	12p13.32	Dual-specificity protein kinase 4	3.938	0.005
Signal	Hs.262886	Inositol polyphosphate-5- phosphatase, 145kD	INPP5D	2q36-q37	Modulating cytokine signaling within the hemopoietic system	3.587	0.009
Signal	Hs.75249	ADP-ribosylation factor-like 6 interacting protein	ARL6IP	16p12-p11.2	Activator of phospholipase D (PLD)	2.801	0.010
Tumor/Suppress	Hs.77793	c-src tyrosine kinase	CSK	15q23-q25	Downregulate the tyrosine kinase activity of the c-src oncoprotein	3.377	0.021
Tumor/Induce	Hs.89839	EphA1	EPHA1	7q34	Overexpression of EPH mRNA was found in a hepatoma	3.039	0.022
Tumor/Induce	Hs.79070	V-myc avian myelocytomatosis viral oncogene homolog	MYC	8q24.12-q24.13	Promotes cell proliferation and transformation	2.357	0.011
Immune response	Hs.118354	Human MHC Class I region proline rich protein mRNA	CAT56	6p21.32	Immune response	2.588	0.024
Miscellaneous	Hs.180610	Splicing factor proline/ glutamine rich	SFPQ	1p34.3	Pre-mRNA splicing factor required for pre-mRNA splicing	10.471	0.006
Miscellaneous/ Cytoskeleton	Hs.75064	Tubulin-specific chaperone c	TBCC	6pter-p12.1	Cofactor in the folding pathway of beta-tubulin	10.2	0.020
Miscellaneous	Hs.438683	BCM-like membrane protein precursor	SBB142	1q23.1	BCM-like membrane protein precursor	3.751	0.004
Miscellaneous	Hs.8203	Endomembrane protein emp70 precursor isolog	LOC56889	10q24.2	Low similarity to human endosomal protein P76	3.502	0.038
Miscellaneous	Hs.311609	Nuclear RNA helicase, DECD variant of DEAD box family	DDXL	19p13.13	Member of the DEAD/H box ATP- dependent RNA helicase family	2.868	0.026
Miscellaneous/ Energy	Hs.150922	BCS1 (yeast homolog)-like	BCS1L	2q33	Function in the assembly of complex III of the respiratory chain	2.682	0.007
Miscellaneous	Hs.6679	hHDC for homolog of Drosophila headcase	LOC51696	6q23-q24	hHDC for homolog of Drosophila headcase	2.611	0.020
Miscellaneous	Hs.5300	Bladder cancer associated protein	BLCAP	20q11.2-q12	Appears to be down-regulated during bladder cancer progression	2.459	0.028
Miscellaneous	Hs.179526	Upregulated by 1, 25-dihydroxyvitamin D-3	VDUP1	1q21.2	Upregulated by 1, 25-dihydroxyvitamin D-3	2.394	0.043
Miscellaneous	Hs.440961	Calpastatin	CAST	5q15-q21	Inhibitor of the cysteine (thiol) protease calpain	2.276	0.000
Miscellaneous	Hs.275775	Selenoprotein P, plasma, 1	SEPP1	5q31	An oxidant defense in the extracellular space	2.186	0.007
EST	Hs.371233	ESTs		Xp22.3	Moderately similar to T08795 hypothetical protein DKFZp586J1822.1	7.826	0.025
EST	Hs.229338	ESTs		X		4.687	0.007
EST	Hs.212957	ESTs		3q26.1	Moderately similar to ZN91_HUMAN ZINC FINGER PROTEIN 91	4.611	0.019
EST	Hs.211823	ESTs		2q37.1		4.519	0.030
EST	Hs.57836	ESTs		17		3.323	0.029
EST	Hs.87912	ESTs		14q24.1		3.314	0.013
EST	Hs.12429	ESTs	FLJ22479	4q26-q27	Hypothetical protein FLJ22479	3.217	0.041
EST	Hs.213586	ESTs		7		2.759	0.044
EST	Hs.2755711	ESTs		22	Weakly similar to T20379 hypothetical protein	2.723	0.019
EST	Hs.191435	ESTs		8p23.1-p22	Weakly similar to S65657 alpha-1C- adrenergic receptor splice form 2	2.638	0.023
EST	Hs.31293	ESTs		9p13.1		2.286	0.035
Predicted protein	Hs.414464	Hypothetical protein	HSD3.1	14q31.3		7.314	0.008
Predicted protein	Hs.100914	Hypothetical protein FLJ10352	FLJ10352	18p11.21		6.239	0.006
Predicted protein	Hs.181112	HSPC126 protein	HSPC126	13q14.12		3.322	0.045
Predicted protein	Hs.306711	KIAA1081 protein	ELKS	12p13.3		3.122	0.036
Predicted protein	Hs.101891	KIAA1193 protein	KIAA1193	19p13.3	Weakly similar to RPB1_HUMAN DNA-directed RNA Pol II largest subunit	3.029	0.030
Predicted protein	Hs.272759	KIAA1457 protein	KIAA1457	12q24.31		2.98	0.020
Predicted protein	Hs.172089	Homo sapiens mRNA; cDNA DKFZp586I2022		11q22.1		2.784	0.036
Predicted protein	Hs.7049	Hypothetical protein FLJ11305	FLJ11305	13q34		2.65	0.028
Predicted protein	Hs.445255	KIAA0368 protein	KIAA0368	9q32		2.423	0.016
Predicted protein	Hs.192190	KIAA0782 protein	KIAA0782	11q13.3		2.332	0.009
Predicted protein	Hs.169910	KIAA0173 gene product	KIAA0173	2p24.3-p24.1	Similar to S72482 hypothetical protein	2.171	0.014

Table 2 Fifty-three differentially up-regulated genes obtained and categorized by their function

Categoty	UniGene	Gene name	Symbol	Locus	Function	Control/HBVinfection	P-value
Signal	Hs.82887	Protein phosphatase 1, regulatory (inhibitor) subunit 11	PPP1R11	6p21.3	Soluble protein phosphatase inhibitor(reppresor)	3.623	0.026
Signal	Hs.437575	TNF receptor-associated factor 2	TRAF2	9q34	Required for activation of NFkappaB	3.23	0.026
Signal	Hs.6527	G protein-coupled receptor 56	GPR56	16q13	Member of the G protein-coupled receptor family	2.817	0.009
Signal	Hs.29203	Homo sapiens G protein beta subunit mRNA, partial cds	GBL	16p13.3	G protein-linked receptor protein for signalling pathway	2.76	0.009
Signal/ Cytoskeleton	Hs.2157	Wiskott-Aldrich syndrome	WAS	Xp11.4-p11.21	Involved in transduction of signals from receptors on the cell surface to the actin cytoskeleton	2.446	0.018
Signal	Hs.440315	Mitogen-activated protein kinase kinase kinase 14	MAP3K14	17q21	Binds to TRAF2 and stimulates NF-kappaB activity	2.185	0.043
Tumor/ Induce	Hs.15243	Nucleolar protein 1 (120kD)	NOL1	12p13.3	Transforms NIH3T3 cells when overexpressed	5.273	0.004
Tumor/ Supress	Hs.9018	Exostoses (multiple)-like 3	EXTL3	8p21	Tumor suppressor, glycosyltransferase activity	5.07	0.093
Tumor/ Supress	Hs.41587	RAD50 (S. cerevisiae) homolog	RAD50	5q31	Associates with MRE11, nibrin (NBS1) and the tumor suppressor BRAC1	2.443	0.013
Growth/ Positive	Hs.511740	Growth differentiation factor 11	GDF11	12q13.13	Regulators of cell growth and differentiation in both embryonic and adult tissues	2.969	0.023
Cell cycle/ Negative	Hs.76364	Allograft inflammatory factor 1	AIF1	6p21.3	Involved in negative regulation of growth of vascular smooth muscle cells	3.573	0.031
Cell cycle/ Positive	Hs.25313	Microspherule protein 1	MCRS1	12q13.12	Involved in cell-cycle-dependent stabilization of ICP22 in HSV1- infected cells	3.273	0.044
Cell cycle/ Positive	Hs.371833	Nuclear receptor binding factor-2	NRBF-2	10	A possible gene activator protein interacting with nuclear hormone receptors	2.568	0.018
Cell cycle/ Positive	Hs.440606	Centrosomal protein 2	CEP2	20q11.22-q12	Regulate centriole-centriole cohesion during the cell cycle	2.422	0.022
Enzyme/ Glycosylation	Hs.4814	Mannosidase, alpha, class 1B, member 1	MAN1B1	9q34	N-linked glycosylation	3.097	0.008
Enzyme/ lysophospholipase	Hs.889	Charot-Leyden crystal protein	CLC	19q13.1	Phospholipid metabolism and anti-pathogen	3.065	0.035
Enzyme/Protease	Hs.75890	Site-1 protease	MBTPS1	16q24	A sterol-regulated subtilisin-like serine protease	2.873	0.023
Immune response	Hs.2014	T cell receptor delta locus	TRD@	14q11.2	T-cell antigen receptor, delta polypeptide	3.69	0.023
Immune response	Hs.465511	Granzyme M	GZMM	19p13.3	Serine protease for anti-pathogen response	3.201	0.023
Transcription	Hs.436871	Zinc finger protein 173	ZNF173	6p21.3	DNA/protein binding, transcriptional protein	3.411	0.002
Transcription	Hs.108139	Zinc finger protein 212	ZNF212	7q36.1	DNA/protein binding, transcriptional protein	2.341	0.045
Apoptosis	Hs.36	Lymphotoxin alpha	LTA	6p21.3	A member of the tumor necrosis factor family	14.912	0.019
Miscellaneous	Hs.434384	Titin	TTN	2q31	Large myofilament protein	4.087	0.012
Miscellaneous	Hs.58927	Nuclear VCP-like	NVL	1q41-q42.2	Member of the AAA family of ATPases	4.005	0.035
Miscellaneous	Hs.122552	G-2 and S-phase expressed 1	GTSE1	22q13.2-q13.3	Accumulates in late S/G2 phase, is phosphorylated in mitosis, and disappears in G1 phase	3.491	0.007
Miscellaneous/Glycosylation	Hs.82921	Solute carrier family 35 (CMP- sialic acid transporter), member 1	SLC35A1	6q15	Important for normal sialylation of glycoproteins and glycolipids	3.352	0.013
Miscellaneous	Hs.410455	Unc119 (C.elegans) homolog	UNC119	17q11.2	May function in photoreceptor neurotransmission	3.328	0.030
Miscellaneous	Hs.55041	CGI-22 protein	MRPL2	6p21.3	Unknown	3.052	0.01
Miscellaneous/Cytoskeleton	Hs.74088	Bridging integrator-3	BIN3	8q21.2	Related to actin assembly- competent state	2.677	0.018
Miscellaneous	Hs.25237	Mesenchymal stem cell protein DSCD75	LOC51337	8q24.3	Moderately similar to uncharacterized Drosophila CG4666	2.615	0.042
EST	Hs.95867	Homo sapiens EST00098 gene, last exon	EST00098	9q34.1		8.781	0.027
EST	Hs.98785	ESTs	KSP37	4p16		3.749	0.011
EST	Hs.136912	ESTs	MGC10796	3q13.13		3.435	0.003
EST	Hs.101774	ESTs	FLJ23045	20p11.23		3.387	0.032
EST	Hs.420262	ESTs		13		3.355	0.022
EST	Hs.124840	ESTs		11q13.1		3.114	0.021
EST	Hs.272299	ESTs	RP4-622L5	1p36.11-p34.2		3.008	0.034
EST	Hs.415048	ESTs		5		2.891	0.025
EST	Hs.531268	ESTs		16		2.889	0.013
EST	Hs.273830	ESTs	FLJ12742	1		2.739	0.020
EST	Hs.190162	ESTs		1p32.3		2.708	0.021
EST	Hs.303172	ESTs		18		2.578	0.04
EST	Hs.59203	ESTs		7		2.437	0.022
EST	Hs.231444	ESTs		1		2.343	0.005
Unknown sequence	Hs.284265	Homo sapiens pRGR1 mRNA, partial cds		6q27		2.966	0.043
Unknown sequence	Hs.291385	Homo sapiens clone 23664 and 23905 mRNA sequence		4p14-p12		2.439	0.041
Predicted protein	Hs.31718	Homo sapiens cDNA FLJ11034 fis, clone PLACE1004258	VRL			17.359	0.000
Predicted protein	Hs.61960	Hypothetical protein	FLJ20040	16p13.3		9.166	0.002
Predicted protein	Hs.274552	Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116	FLJ10720	5		4.751	0.015
Predicted protein	Hs.279761	HSPC134 protein	HSPC134	14q11.2		3.501	0.038
Predicted protein	Hs.283716	Hypothetical protein PRO1584	PRO1584	8p21.2		3.493	0.033
Predicted protein	Hs.464526	Homo sapiens clone 23649 and 23755 unknown mRNA, partial cds		18q11.2		3.198	0.032
Predicted protein	Hs.274412	Homo sapiens cDNA FLJ10207 fis, clone HEMBA1005475	UPF3A	17p11.2		3.076	0.012