Gene expression profiles in an hepatitis B virus transfected hepatoblastoma cell line and differentially regulated gene expression by interferon-α

Table 1 Comparison of microarray and RNA slot analyses on 4 selected genes

Accession	X67325		AB023136		AA622328		NM_018300
ID	Ratio of arrays	Ratio of slot	Ratio of arrays	Ratio of slot	Ratio of arrays	Ratio of slot	Ratio of arrays	Ratio of slot
6 h/0 h	3.6	Undetectable	3.4	1.3	2.0	0.5	1.1	2.9
24 h/0 h	5.9	> 31	7.2	3.5	3.9	1.6	4.9	3.4
48 h/0 h	6.1	> 33	8.4	6.2	3.8	5.7	1.0	1.3
Description	IFN-inducible P27		Sec15B(vesicle traffic protein)		beta3gal-T5 gene		cDNA FLJ12673

Table 2 Gene expression profiling in the microarray analysis

Ratio	Gene differences in HepG22.2.15			Gene differences in HepG2			Gene differences in HepG22.2.15/HepG2
	6 h/0 h	24 h/0 h	48 h/0 h	6 h/0 h	24 h/0 h	48 h/0 h	0 h	6 h	24 h	48 h
3	34	48	45	83	103	48	89	40	33	36
5	10	18	12	37	37	23	27	12	8	11

Table 3 Differently expressed known genes in HepG₂ 2.2.15 and HepG₂ cell lines before IFN-α treatment

Accession ID	HepG2	HepG22.2.15	Ratio	Description	Unigene
Cell cycle
Y13467	101.95	29.54	-3.45	RB18A	Hs.15589
Ligands and receptors
AF022375	16.17	5.19	-3.12	vascular endothelial growth factor	Hs.73793
Phosphatase
U12128	152.03	27.26	-5.58	tyrosine phosphatase 1E (PTP1E)	Hs.211595
Transcription factors
D87258	156.76	37.78	-4.15	serin protease with IGF-binding motif	Hs.75111
Miscellaneous
X69962	242.93	73.77	-3.29	FMR-1	Hs.89764
X56597	1.64	21.98	13.40	humFib mRNA for fibrillarin	Hs.99853
U76713	403.90	123.59	-3.27	apobec-1 binding protein 1	Hs.81361
U50410	189.94	27.03	-7.03	heparan sulphate proteoglycan (OCI5)	Hs.119651
U23070	5.35	16.82	3.14	putative transmembrane protein (nma)	Hs.78776
S68805	4.12	12.74	3.09	L-arginine:glycine amidinotransferase	Hs.75335
M22430	13.63	50.17	3.68	RASF-A PLA2	Hs.76422
M16961	221.65	61.50	-3.60	alpha-2-HS-glycoprotein alpha and beta chain	Hs.75430
M13928	21.15	163.32	7.72	delta-aminolevulinate dehydratase	Hs.1227
L40157	14.58	92.98	6.38	endosome-associated protein (EEA1)	Hs.2864
L24123	1 309.05	430.92	-3.04	NRF1 protein (NRF1)	Hs.83469
D00096	7.61	31.28	4.11	Prealbumin	Hs.194366
AJ006835	150.29	49.21	-3.05	U17 small nucleolar RNA host gene	Hs.196769
AF073308	237.11	78.45	-3.02	nonsyndromic hearing impairment protein (DFNA5)	Hs.13530
AF050127	823.97	71.21	-11.57	hypoxia inducible factor (aHIF)	Hs.197540
AC002045	237.87	67.71	-3.51	Chromosome 16 BAC clone CIT987SK-A-589H1	Hs.253182
AB027013	15.62	2.31	-6.76	Nucleosome Assembly Protein 1-like 2	Hs.66180
AB023136	544.25	44.18	-12.32	KIAA0919	Hs.44175

Table 4 Functional catalogues of 3 fold regulated genes in HepG₂ and HepG₂ 2.2.15 cell lines post IFN-α treatment

Catalogue	3-fold regulated gene number in HepG22.2.15			3-fold regulated gene number in HepG2
	6 h/0 h	24 h/0 h	48 h/0 h	6 h/0 h	24 h/0 h	48 h/0 h
Cell cycle	-	1	1	-	-	-
Coagulation	-	1	1	-	1	-
Cytokine/receptors	1	2	2	1	1	-
Extracellular matrix and cell adhesion	-	-	1	-	1	-
GTP binding proteins and signal transduction	2	-	1	-	1	1
Interferon	8	6	3	6	5	5
Kinase and phosphatase	-	-	1	-	2	-
Ligands and receptors	-	1	2	-	-	-
Mitochondrial	-	1	1	-	2	-
Phosphatase and phosphodiesterase	2	2	2	1	2	1
Protooncogenes	-	1	-	1	-	-
Transcription factors	-	-	-	1	1	1
Viral and clathrin receptors	-	1	1	-	1	-
Miscellaneous	7	8	8	14	18	13
New ESTs	14	24	21	59	68	27
Total	34	48	45	83	103	48

Table 5 Kinetics of IFN-treated gene expression profiles in 23 selected genes from HepG₂ and HepG₂2.2.15 cells

Accession ID	HepG22.2.15 cell lines			HepG2 cell lines			Description
	6 h/0 h	24 h/0 h	48 h/0 h	6 h/0 h	24 h/0 h	48 h/0 h
Interferon
X57352	3.8	3.1	2.5	6.5	8.1	6.4	1-8U gene from interferon-inducible gene family
X57351	3.4	2.2	2.2	4.3	4.4	4.4	1-8U gene from interferon-inducible gene family
M87503	2.3	1.7	1.7	3.2	2.4	2.6	IFN-responsive transcription factor subunit
M33882	2.4	1.6	1.5	2.5	2.1	1.6	p78 protein
M11810	9.1	5.7	4.4	8.4	7.7	3.9	(2’-5’) oligo A synthetase E gene
L07633	2.0	1.3	1.5	2.0	2.7	1.3	(clone 1950.2) interferon-gamma IEF SSP 5111
J04164	6.7	5.0	2.9	6.4	7.0	6.5	Interferon-inducible protein 9-27
D28137	3.0	3.3	2.8	2.7	2.6	1.8	BST-2
AJ225089	3.9	1.3	1.1	1.9	2.1	1.2	2’-5’ oligoadenylate synthetase 59 kDa isoform
Kinase/Phosphate
U07358	-1.3	-1.3	-2.5	1.1	2.4	1.4	Protein kinase (zpk)
U02680	-1.1	1.4	-2.5	1.5	7.1	1.6	Protein tyrosine kinase
AF032437	-1.1	-2.5	-1.7	-1.3	-3.3	-2.0	Mitogen activated protein kinase activated protein kinase
Ligands and receptors
D86096	2.3	4.6	3.5	1.9	1.8	2.3	Prostaglandin E receptor EP3 subtype
AF022375	1.8	1.8	3.2	-1.2	-1.1	1.1	Vascular endothelial growth factor
Phosphatase
U12128	3.0	4.8	4.7	-1.2	-1.1	-1.2	Protein tyrosine phosphatase 1E (PTP1E)
Protein degradation
Z14977	2.2	1.2	1.4	2.7	1.3	1.6	Major histocompatibility complex encoded
							proteasome subunit LMP2
AF061736	2.6	1.5	1.4	2.3	2.3	2.0	Ubiquitin-conjugating enzyme RIG-B
Protooncogenes
U52969	1.1	-2.0	-1.3	2.2	1.6	2.1	PEP19 (PCP4)
U50529	-2.5	-5.0	-2.5	1.7	1.5	2.2	BRCA2 region, mRNA sequence CG016
Transcription factors
D87258	1.6	2.3	2.5	1.0	-1.1	-1.5	Serin protease with IGF-binding motif
Viral and clathrin receptors
X81636	1.1	5.5	5.2	-1.1	6.4	-1.7	Clathrin light chain a
U70321	-1.3	-2.0	1.1	2.0	1.2	1.6	Herpesvirus entry mediator
AF079221	1.0	1.2	2.9	1.7	2.2	1.9	BCL2/adenovirus E1B 19kDa-interacting protein 3 a