Table 5.

Differentially expressed genes in HCC cell lines.

Downregulated genes
AFFY_ID	Gene	Gene symbol	mRNA NCBI accession numbera	Foldb	P valuec	Chromosomal location	Chromosomal aberration in HCCd	Epigenetic regulation in HCC
203400_s_at	Transferrin	TF	NM_001063	−8.988	0.042	3q22.1	3q22–24 (gain)
219465_at	Apolipoprotein A-II	APOA II	NM_001643	−8.932	0.050	1q21–q23	1q21–23 (gain)
219466_s_at	Apolipoprotein A-II	APOA II	NM_001643	−8.686	0.026	1q21–q23	1q21–23 (gain)
205892_s_at	Fatty acid binding protein 1, liver	FABP1	NM_001443	−7.260	0.048	2p11
209560_s_at	Delta-like 1 homolog (Drosophila)	DLK1	NM_003836 and NM_001032997	−6.914	0.017	14q32		Upregulation due to deregulation of methylation
224588_at	X (inactive)-specific transcript	XIST	BX648323	−6.746	0.002	Xq13.2
214218_s_at	X (inactive)-specific transcript	XIST	BX648323	−5.244	0.034	Xq13.2
217073_x_at	Apolipoprotein A-I	APOA I	NM_000039	−6.390	0.027	11q23–q24	11q23.1 (AI)
209505_at	Nuclear receptor subfamily 2, group F, member 1	NR2F1	NM_005654	−5.292	0.054	5q14
209459_s_at	4-Aminobutyrate aminotransferase	ABAT	NM_020686 and NM_000663	−5.195	0.020	16p13.2	16p13 (AI)
242375_x_at	Phenylalanine hydroxylase	PAH	NM_000277	−5.103	0.015	12q22–q24.2	12q22–q23 (breakpoints of chromosome rearrangement)
204059_s_at	Malic enzyme 1, NADP(+)-dependent, cytosolic	ME1	NM_002395	−5.029	0.038	6q12
200824_at	Glutathione S-transferase pi	GSTP1	NM_000852	−4.999	0.045	11q13		Silenced by hypermethylation
225424_at	Glycerol-3-phosphate acyltransferase, mitochondrial	GPAM	NM_020918	−4.771	0.008	10q25.2
206130_s_at	Asialoglycoprotein receptor 2	ASGR2	NM_001181, NM_080912, NM_080913, and NM_080914	−4.510	0.044	17p	17p1–p2 (MDR); 17p13.1 (LOH of p53 locus); 17p11.2–p13.3 (AI); 17p12-pter (LOH)
205352_at	Serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1	SERPINI1	NM_005025	−4.484	0.043	3q26.1	3q25-qter (gain)
211237_s_at	Fibroblast growth factor receptor 4	FGFR4	NM_002011, NM_022963, and NM_213647	−4.228	0.050	5q35.1-qter	5q35-qter (LOH)
201917_s_at	Hypothetical protein FLJ10618 (solute carrier family 25, member 36)	SLC25A36	NM_018155	−3.026	0.031	3q23
201918_at	Hypothetical protein FLJ10618 (solute carrier family 25, member 36)	SLC25A36	NM_018155	−2.862	0.043	3q23
207819_s_at	ATP-binding cassette, sub-family B (MDR/TAP), member 4	ABCB4	NM_000443, NM_018849, and NM_018850	−2.035	0.001	7q21.1	7q21–32 (gain); 7q21.3–7q22 (amplification of CYP3A locus)
213198_at	Activin A receptor, type IB	ACVR1B	NM_004302, NM_020327, and NM_020328	−1.963	0.023	12q13
1552474_a_at	Guanidinoacetate N-methyltransferase	GAMT	NM_000156, and NM_138924	−1.749	0.023	19p13.3	19p13.3 (AI)
219569_s_at	Transmembrane protein 22	TMEM22	NM_025246	−1.487	0.007	3q22.3	3q22–24 (gain)
Upregulated genes
44120_at	aarF domain containing kinase 2	ADCK1	NM_020421	1.349	0.037	14q24.3	14q24–q32 (LOH in less than 10% of HCC cases)
228737_at	Chromosome 20 open reading frame 100 (TOX high mobility group box family member 2)	TOX2	NM_032883	1.937	0.025	20q13.12
219587_at	Tetratricopeptide repeat domain 12	TTC12	NM_017868	2.192	0.016	11q23.1	11q23.1 (AI)
212295_s_at	Solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	SLC7A1	NM_003045	2.323	0.034	13q12–q14	13q13–14 (LOH of Rb locus); 13q12.1–q12.3 (AI); 13q12–q13 (deletion of BRCA2 locus); 13q13.3 –q22.1 (loss)
219582_at	Opioid growth factor receptor-like 1	OGFRL1	NM_024576	2.582	0.026	6q13
233540_s_at	CDK5 regulatory subunit associated protein 2	CDK5RAP2	NM_018249 and NM_001011649	2.812	0.054	9q33.2	9p13–9q33 (LOH)
212607_at	v-akt Murine thymoma viral oncogene homolog 3 (protein kinase B, gamma)	AKT3	NM_005465 and NM_181690	2.832	0.002	1q43–q44	Amplification of AKT3 gene
208502_s_at	Paired-like homeodomain transcription factor 1	PITX1	NM_002653	3.178	0.032	5q31	5q31 (amplification of SMAD5 gene)
201189_s_at	Inositol 1,4,5-triphosphate receptor, type 3	ITPR3	NM_002224	3.315	0.011	6p21
217339_x_at	Cancer/testis antigen 1	CTAG1	NM_139250 and NM_001327	3.650	0.020	Xq28
211966_at	Collagen, type IV, α 2	COLIVa2	NM_001846	3.743	0.038	13q34	13q34 (gain)
225147_at	Pleckstrin homology, Sec7 and coiled-coil domains 3	PSCD3	NM_004227	3.830	0.049	7p22.1
1552390_a_at	Hypothetical protein FLJ39553	C8orf47	NM_173549	3.922	0.033	8q22.2	8q22–24 (gain)
241418_at	cDNA DKFZp686B14224 (from clone DKFZp686B14224)	LOC344887	BX640843	4.222	0.029	3q27.2	3q25-qter (gain)
1553830_s_at	Melanoma antigen, family A, 3	MAGEA3	NM_005362	4.296	0.007	Xq28	Demethylation of MAGEA3 gene
212223_at	Iduronate 2-sulfatase (Hunter syndrome)	IDS	NM_000202 and NM_006123	4.413	0.029	Xq28
219279_at	Dedicator of cytokinesis 10	DOCK10	NM_014689	4.716	0.039	2q36.2
223642_at	Zic family member 2 (odd-paired homolog, Drosophila)	ZIC2	NM_007129	4.745	0.025	13q32	13q32-qter (AI); 13q31–34 (gain)
204341_at	Tripartite motif-containing 16	TRIM16	NM_006470	4.933	0.008	17p11.2	17p11.2–p13.3 (AI)
208966_x_at	Interferon, γ-inducible protein 16	IFI16	NM_152501, NM_198928, NM_198929, and NM_198930	5.510	0.037	1q22	1q21–q22 (gain); 1q22–q23 (gain)
209288_s_at	CDC42 effector protein (Rho GTPase binding) 3	Cdc42ep3	NM_006449	5.802	0.015	2p21
200600_at	Moesin	MSN	NM_002444	6.446	0.012	Xq11.2-q12
204955_at	Sushi-repeat-containing protein, X-linked	SRPX	NM_006307	6.835	0.020	Xp21.1	Xp21-pter (gain)
201105_at	Lectin, galactoside-binding, soluble, 1 (galectin 1)	LGALS1	NM_002305	6.850	0.005	22q13.1	Hypomethylation of LGALS1 gene
225275_at	EGF-like repeats and discoidin I-like domains 3	EDIL3	NM_005711	7.133	0.009	5q14
204268_at	S100 calcium binding protein A2	S100A2	NM_005978	7.183	0.039	1q21	1q21–23 (gain)
209160_at	Aldo-keto reductase family 1, member C3 (3-α hydroxysteroid dehydrogenase, type II)	AKR1C3	NM_003739	7.595	0.024	10p15-p14

^aFor the genes that have alternatively spliced variants the NCBI accession numbers of each alternatively spliced variant are shown.

^bThe changes in gene expression of JHH6 versus HuH7 are shown as log2.

^cP value adjusted according to the Bonferroni method.

^dLOH, loss of heterozygosity; MDR, minimal delition region; AI, allelic imbalance.