Table 5.
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 |
For the genes that have alternatively spliced variants the NCBI accession numbers of each alternatively spliced variant are shown.
The changes in gene expression of JHH6 versus HuH7 are shown as log2.
P value adjusted according to the Bonferroni method.
LOH, loss of heterozygosity; MDR, minimal delition region; AI, allelic imbalance.