Modulation of gene expression in MHCC97 cells by interferon alpha

Table 1 Primer sequence and condition for PCR analysis of selected genes

Category	Gene	Sense and antisense primers	Annealing(°C)	Cycles	Size(bp)
Cytoskeletal gene	Neutral calponin	5’-TGGCACCAGCTAGAAAACCT-3’; 5’-CAGGGACATGGAGGAGTTGT-3’	56	26	498
Proliferative gene	hMCM2	5’-ACCGAGACAATGACCTACGG-3’; 5’-CTAGCTGTCTGCCCCTTGTC-3’	56	30	382
Angiogenic gene	VEGF165 receptor	5’-GAAGCACCGAGAGAACAAGG-3; 5’-CACCTGTGAGCTGGAAGTCA-3’	56	30	359
IFN-α-induced genes	9-27	5’-TTGGTCCCTGGCTAATTCAC-3’; 5’-ATGAGGATGCCCAGAATCAG-3’	53	35	491
	ISG-56 ku	5’-AAAAGCCCACATTTGAGGTG-3’; 5’-GGCTGATATCTGGGTGCCTA-3’	54	30	451
MAPK pathway-related genes	ERK activator kinase (MEK2)	5’-CGAAAGGATCTCAGAGCTGG-3’; 5’-GTGCTTCTCTCGGAGGTACG-3’	56	26	349
	G3BP2	5’-GCAGAACCTGTTTCTCTGCC-3’; 5’-CACCACCACCTCTGGTTTCT-3’	56	30	475
	CHED	5’-TCCTTGGCGAACTCTTCACT-3’; 5’-TGCCATAAAGGGAGATCTGG-3’	56	30	336
cAMP/PI3 pathway-related gene	Adenylyl cyclase	5’-CCAGGAGCCTGAAGAATGAG-3’; 5’-GGCTTCTGAGCTCCAATCAC-3’	53	35	439
Housekeeping gene	γ-Actin	5’-ATGGAAGAAGAAATCGCCGC-3’; 5’-ACACGCAGCTCGTTGTAGAA-3’	55	25	287

Table 2 Gene expression profile of MHCC97 cells induced by IFN-α

Category	GenBank ID	Gene description	Cy5/Cy3* (average)
2.1 Metabolism related genes	HUMCRTR	Creatine transporter	0.251
	HSGAGMR	GARs-AIRs-GART	0.289
	HUM2OGDH	2-Oxoglutarate dehydrogenase	0.298
	AF034544	Delta7-sterol reductase	0.318
	HUMTK	Thymidine kinase	0.333
	HSU12778	Acyl-CoA dehydrogenase	0.341
	HUMTHBP	Thyroid hormone-binding protein(p55)	0.349
	AF067127	7-Dehydrocholesterol reductase (DHCR)	0.356
	HSPRCOX	Pristanoyl-CoA oxidase	0.364
	AF035429	Cytochrome oxidase subunit 1	0.372
	AF070544	Glucose transporter glycoprotein (SGLT)	0.379
	HSPFKLA	Liver-type1-phosphofructokianse (PFKL)	0.392
	HUMSHMT	Serine hydroxymethyltransferase 2 (SHMT2)	0.407
	HUMMGPHB	Brain glycogen phosphorylase	0.413
	HUMTCBA	Cytosolic thyroid hormone-binding protein (p58)	0.415
	D88152	Acetyl-coenzyme A transporter	0.451
	HUMPKM2L	M2-type pyruvate kinase	0.456
	HSLDHBR	Lactate dehydrogenase B	2.156
	AF108211	Inorganic pyrophosphatase	2.25
	HSCOXVII	Cytochrome C oxidase VII	2.279
	HUMCYCPSK	Cytochrome C (HS7)	2.574
	HUMDBI	Diazepam binding inhibitor	2.628
2.2 Proliferation, apoptosis and damaged DNA repairing related genes	HSATPBR	Na/K ATPase beta subunit	0.208
	HUMP53T	Mutant p53 protein	0.233
	HSMITG	Mitochondrial DNA	0.309
	HSNUMAMR	Nuclear mitotic apparatus protein	0.325
	HSDNALIG3	DNA ligase III	0.34
	G28520	STS HSGC-31478 (homolog to Rad23a)	0.341
	AF096870	Estrogen-responsive B box protein	0.352
	AF001609	EXT like protein 3	0.367
	AF015283	Selenoprotein W	0.369
	AF011905	Putative checkpoint control protein hRad1	0.398
	HUMHMAM2	Minichromosome maintenance 2	0.408
	HUMRNAPII	RNA polymerase II 23 ku subunit	0.408
	AF007790	Inversely correlated with estrogen receptor Expression (ICERE-1)	0.413
	HSU78310	Pescadillo	0.43
	AF004162	Nickel-specific induction protein (Cap43)	0.434
	HSU3298	UV-damaged DNA binding factor	0.437
	HUMP1CDC47	P1cdc47	0.442
	HSU72649	B cell translocation gene 2	0.444
	AF031523	bcl-xL/bcl-2 associated death promoter (BAD)	0.481
	AF132973	CGI-39 (homolog to GRIM-19)	2.079
2.3 Morphogenesis, adhesion, and cytoskeleton	D38735	Neutral calponin	0.141
	AF006082	Actin-related protein Arp2	0.197
	U01244	Fibulin 1D	0.212
remodeling related genes	AF070593	Beta tublin	0.236
	HSU35622	EWS-E1A-F chimeric protein	0.255
	AF049259	Keratin 13	0.335
	HSPRO4HY	Prolyl 4-hydoxylase beta	0.337
	HUMCN4GEL	Collagenase type IV	0.36
	AF005654	Actin-binding double zinc-finger protein	0.378
	HSTEST	Testican	0.379
	HUMEPSURAN	Surface antigen	0.389
	AF004841	CAM-related/down-regulated by oncogenes	0.398
	HUMGLBA	Co-beta-glucosidase	0.402
	HUMCA1XIA	Alpha-1 type XI collagen	0.423
	HUMMCPGV	Macrophage capping protein	0.461
	HUMNID	Nidogen	0.497
	HSTUMP	Translationally controlled tumor protein	2.022
2.4 Signal transmitting related genes	HUMEPHT2R	Protein tyrosine kinase (NET PTK)	0.248
	HUMMEK2NF	ERK activator kinase (MEK2)	0.271
	HUMBADPTA	Beta-adaptin	0.273
	HUMP2A	Alpha-PR65	0.282
	HUMHRGAA	rab GDI alpha	0.285
	AF053535	ras-GAP/RNA binding protein G3BP2	0.296
	HSRING3GE	RING 3	0.316
	HSU45973	Pt Ins (4,5) P(2) 5-phosphatase	0.324
	HSU07139	Voltage-gated calcium channel beta	0.329
	HUMFTPB	Farnesyl-protein transferase beta	0.345
	HSU33053	Lipid-activated protein kinase (PRK1)	0.352
	HUMHK1A	Calcium-ATPase (HK1)	0.386
	HSU66406	EPH-related PTK receptor ligand LERK-8	0.386
	HSPP15	Placental protein 15	0.387
	HSADCYCL	Adenylyl cyclase	0.409
	HUMCHED	cdc2-related protein kinase (CHED)	0.412
	AF093265	Homer 3	0.415
	HSU40282	Integrin-linked kinase	0.416
	HUMGKAS	Stimulatory G protein	0.416
	HSU43939	Nuclear transport factor 2	0.429
	HUMCAK	Tyrosine protein kinase (CAK)	0.439
	HUMGNOS48	Endothelial nitric oxide synthase	0.443
	HUMCDPKIV	Calmodulin-dependent protein kinase IV	0.449
	HSPKX1MR	Protein kinase, PKX1	0.469
	D83760	Mother against dpp (Mad) related protein	0.472
	HUMEGFGRBA	EGF receptor binding protein GRB2	0.481
	HSU51004	Protein kinase C inhibitor (PKCI-1)	2.223
2.5 Tumor angiogenesis related genes	HUMRNAMBPE	Golli-mbp	0.236
	AF016050	VEGF 165 receptor/neuropilin	0.25
	AF001307	Aryl hydrocarbon receptor nuclear translocator	0.27
	HSU64791	Golgi membrane sialoglycoprotein MG 160	0.355
	HUMPTPRZ	Protein tyrosine phosphatase Zeta-polypeptide	0.363
	HSU28811	Cysteine-rich FGFR (CFR1)	0.414
	HSU20758	Osteopontin	2.193
	HUMTR107	DNA-binding protein, TAXREB107	2.24
	HUMNEPPON	Nephropontin	2.413
2.6 Transcriptional activity related genes	S66431	Retinoblastoma binding protein 2	0.182
	HUMANT61K	Medium antigen-associated 61 ku protein	0.183
	HSU58197	Interleukin enhancer binging factor 2	0.226
	HSUBP	Upstream binding factor	0.266
	4758315	ets-related molecule, ETV5	0.267
	AF099013	Glucocorticoid modulatory element binding protein 1	0.309
	HSU72621	Lost on transformation 1(LOT1)	0.313
	HUMFOS	Oncogene protein, c-fos	0.361
	AB019524	Nuclear receptor co-repressor	0.369
	HS14AGGRE	Conserved gene telomeric to alpha globin cluster	0.398
	HSU74667	tat interactive protein (tip60)	0.404
	AF114816	KRAB-zinc finger protein SZF1-1	0.406
	HSU80456	Drosophila single-minded, SIM2	0.409
	AF117756	TRAP 150	0.41
	HSU15306	Cysteine rich DNA binding protein NFX1	0.417
	S57153	Retinoblastoma binding protein 1	0.469
	HUM56KDAPR	IEF SSP 9502	2.183
	HUMTR107	DNA binding protein. TAXREB 107	2.24
	HUMMSS1	Mammalian suppressor of sgv 1, MSS 1	2.313
2.7 mRNA and protein processing, secretory, proteolysis related genes	HSU39412	Alpha SNAP	0.141
	HSU47927	Isopeptidase T (ISOT)	0.229
	HSU72355	hsp27 ERE-TATA bind protein, HET	0.231
	AF077039	TIM17 homolog	0.238
	HUMHRH1	RNA helicase, HRH1	0.251
	AF206402	U5 SnRNP 100 ku protein	0.255
	D85429	Heat shock protein 40	0.344
	HSU85946	hSec 10p	0.378
	HSY10806	Arginine methyltransferase	0.412
	AB002135	Glycophosphatidylinositol anchor attachment 1	0.428
	AB007510	PRP8 protein	0.436
	HSU24105	Coatomer protein (COPA)	0.455
	HSCANPX	Calpain-like protease (CANPX)	0.456
	HSRBPRL7A	Ribosomal protein L7	2.067
	D89678	A+U-rich element RNA-binding protein	2.069
	HSU14966	Ribosomal protein L5	2.113
	HSRPL31	Ribosomal protein L31	2.142
	HUMPSC9	Proteasome subunit HC9	2.179
	HSU26312	Heterochromatin protein HP1 HS-gamma	2.182
	HUMRPS7A	Ribosomal protein S7	2.289
	AF106622	TIM17a	2.312
	HSUCEH3	Ubiquitin-conjugated enzyme UbCH2	2.323
	HUMRPS7A	Ribosomal protein S7	2.289
	AF106622	TIM17a	2.312
	HSUCEH3	Ubiquitin-conjugated enzyme UbCH2	2.323
	HUMRPS25	Ribosomal protein S25	2.326
	HUMRPSA3A	Ribosomal protein S3a	2.328
	HSRNASMG	Sm protein G	2.334
	HUMRPS18	Ribosomal protein S18	2.341
	HUMRP4SX	Ribosomal protein S4 isoform	2.346
	HUMPSC3	Proteasome subunit HC3	2.368
	HUMTCP20	Chaperonin protein, TCP20	2.572
	4504522	Chaperonin protein, hsp10	2.686
2.8 Tumor antigen processing, anti-viral infection related genes	HUMSAPC1	Cerebroside sulfate activator protein	0.211
	AF077011	Interleukin 16	0.23
	AF057307	Prosaposin	0.26
	HUMSIATA	Sialyltransferase	0.26
	AF055008	Epithelin 1 and 2	0.363
	HSU58766	FX protein	0.393
	HUMOSF1	OSF1	0.407
	HSU46194	RAGE 4	0.43
	HSU18121	136 ku double-stranded RNA binding protein	0.469
	AF021315	Reverse transcriptase	0.483
	S74095	Preproenkephalin A	2.115
	HUM927A	Interferon inducible protein 9-27	2.356
	HSIFI56R	Interferon inducible protein 56 ku	3.829
	HUMHCAMAP1	Interferon inducible protein 44 ku	4.03
2.9 Genes with unknown biological functions	D50928	KIAA0138	0.23
	AF132942	CGI08	0.269
	AB020677	KIAA0870	0.271
	AB011110	KIAA0538	0.277
	AB028956	KIAA1033	0.28
	HSU10362	GB36b glycoprotein	0.335
	4579277	A homolog of proteasome regulatory S2	0.352
	AB002356	KIAA0358	0.371
	4505130	A homolog of MCM3	0.371
	AB029020	KIAA1097	0.381
	HS130N43		0.383
	HSU66406	Eplg8	0.386
	HSNIPSNA1	NIPSNAP1 protein	0.391
	AB002378	KIAA0380	0.405
	HSU90907	Regulatory subunit of P55 PIK	0.407
	AB208959	KIAA1036	0.414
	AB020658	KIAA0851	0.416
	AF035282		0.416
	AF000136		0.419
	HUMORFFA	KIAA0120	0.424
	D13699	KIAA0019	0.43
	HUMORFB1	KIAA0123	0.432
	AF151830	CGI72	0.436
	AB007900	KIAA0440	0.437
	AB014595	KIAA0695	0.439
	HSM800064		0.439
	HUMORFA04	KIAA0115	0.457
	HSU79287		0.462
	AF007149		0.473
	AF007135		2.147
	AF151875	CGI117	2.184
	AF151857	CGI99	2.326
	HUMRSC508	KIAA0020	2.45