Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip

doi:10.3748/wjg.v11.i10.1463

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Mar 14, 2005 (publication date) through Apr 18, 2024

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World Journal of Gastroenterology

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1007-9327

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

Liver Cancer

World J Gastroenterol. Mar 14, 2005; 11(10): 1463-1472
Published online Mar 14, 2005. doi: 10.3748/wjg.v11.i10.1463

Table 1 Differential gene expression profile in cell lines Hca-F vs Hca-P.

Gene	Symbol descriptions	F vs P_Signal log ratio
Slc38a4	Solute carrier family 38, member 4
	¹gb: NM_027052	9
	gb: AK003626	3.4
Krt2-8	Keratin complex 2, basic, gene 8
	gb: M21836	8.6
	gb: NM_031170	4.8
Krt1-19	Keratin complex 1, acidic, gene 19	7.4
Cldn9	Claudin 9	7.4
Gja1	Gap junction membrane channel protein alpha 1
	gb: M63801	7.2
	gb: BC006894	6.4
Fbp2	Fructose bisphosphatase 2	7.1
R75183	Expressed sequence R75183
	gb: BC004774	7
	gb: BB324973	5.5
Egfr	Epidermal growth factor receptor
	gb: AF275367	6.9
	gb: U03425	3.6
Lepr	Leptin receptor	6.7
Tm4sf3	Transmembrane 4 superfamily member 3	6.5
Pla2g1b	Phospholipase A2, group IB, pancreas	6.4
Ripk3	Receptor-interacting serine-threonine kinase 3	6.4
Igfbp4	Insulin-like growth factor binding protein 4
	gb: NM_010517	6.3
	gb: BC019836 21423756_s_at	5.8
	gb: BC019836 1423757_x_at	4.1
	gb: AA119124	4
Piwil2	Piwi-like homolog 2 (Drosophila)	6.3
IL24	Interleukin 24	5.9
Daf1	Decay accelerating factor 1	5.9
Cav	Caveolin, caveolae protein	5.8
Arhgef3	Rho guanine nucleotide
	exchange factor (GEF) 3	5.7
Efna1	Ephrin A1
	gb: D38146	5.7
	gb: BC002046	4.2
Ptpn8	Protein tyrosine phosphatase,
	non-receptor type 8	5.6
Rab3b	RAB3B, member RAS oncogene family	5.6
1190003K14Rik	RIKEN cDNA 1190003K14 gene	5.6
Sh3bp5	SH3-domain binding protein 5
	(BTK-associated)	5.5
Fscn1	Fascin homolog 1, actin bundling protein
	(Strongylocentrotus purpuratus)
	gb: NM_007984 1416514_a_at	5.4
	gb: BE952057	4.2
	gb: NM_007984 1448378_at	3.7
Fgf15	Fibroblast growth factor 15	5.4
Ehox	ES cell derived homeobox containing gene	5.3
Ankrd1	Ankyrin repeat domain 1 (cardiac muscle)
	gb: NM_013468	5.3
	gb: AK009959	3.6
1600023A02Rik	RIKEN cDNA 1600023A02 gene	5.3
Cd109	CD109 antigen	5.3
BC037006	cDNA sequence BC037006	5.3
Ltb4dh	Leukotriene B4 12-hydroxydehydrogenase	5.2
Krt2-7	Keratin complex 2, basic, gene 7	5.2
Cnn2	Calponin 2	5.2
Sema3b	Sema domain, immunoglobulin domain (Ig),
	short basic domain, secreted, (semaphorin) 3B
	gb: BB116052	5.1
	gb: NM_009153	4.7
Krt1-18	Keratin complex 1, acidic, gene 18	5.1
	Mouse gene for 18S rRNA	5.1
Fosl1	Fos-like antigen 1
	gb: NM_010235	5
	gb: U34245	4.4
Sncg	Synuclein, gamma	5
Col8a1	Procollagen, type VIII, alpha 1	4.9
Pcdhb7	Protocadherin beta 7	4.9
Msln	Mesothelin	4.9
IL23a	Interleukin 23, alpha subunit p19	4.9
	Mus musculus adult male tongue cDNA	4.8
Ppp1r14a	Protein phosphatase 1, regulatory
	(inhibitor) subunit 14A	4.7
Csf3	Colony stimulating factor 3 (granulocyte)	4.7
Nfil3	Nuclear factor, interleukin 3, regulated	4.6
Procr	Protein C receptor, endothelial	4.6
Nr1d1	Nuclear receptor subfamily 1,
	group D, member 1	4.6
2810003C17Rik	RIKEN cDNA 2810003C17 gene	4.6
MGC27770	Hypothetical protein MGC27770	4.5
Eng	Endoglin	4.5
F2r	Coagulation factor II (thrombin) receptor	4.5
Cdc42ep5	CDC42 effector protein
	(Rho GTPase binding) 5	4.4
Pla2g7	Phospholipase A2, group VII
	(platelet-activating factor
	acetylhydrolase, plasma)	4.4
D18Ertd653e	DNA segment, Chr 18,
	ERATO Doi 653, expressed	4.4
IL2rg	Interleukin 2 receptor, gamma chain
	gb: L20048 1416296_at	4.3
	gb: L20048 1416295_a_at	3.3
Smpd2	Sphingomyelin phosphodiesterase 2, neutral	4.3
Areg	Amphiregulin	4.3
Mcam	Melanoma cell adhesion molecule	4.2
Rtn2	Reticulon 2 (Z-band associated protein)	4.2
Gcnt2	Glucosaminyltransferase, I-branching enzyme	4.2
D7Ertd458e	DNA segment, Chr 7, ERATO Doi 458, expressed
	gb: NM_009310	4.2
	gb: BB049138 1423904_a_at	4
	gb: BC013673 1451160_s_at	4
	gb: BB049138 1423905_at	3.9
	gb: BC013673 1423903_at	3.8
Chi3l3	Chitinase 3-like 3	4.1
D4Ertd765e	DNA segment, Chr 4,
	ERATO Doi 765, expressed	4.1
Ptpr	Protein tyrosine phosphatase, receptor type, R	4.1
Scn8a	Sodium channel, voltage-gated, type VIII,
	alpha polypeptide	4
AXL	AXL receptor tyrosine kinase	4
Serpinh1	Serine (or cysteine) proteinase inhibitor,
	clade H, member 1	4
Panx1	Pannexin 1	3.9
Tm4sf9	Transmembrane 4 superfamily member 9	3.9
Mak	Male germ cell-associated kinase	3.9
	Mus musculus transcribed sequences	3.8
9130017N09Rik	RIKEN cDNA 9130017N09 gene	3.8
Loxl2	Lysyl oxidase-like 2	3.7
Dok1	Downstream of tyrosine kinase 1	3.6
Abhd3	Abhydrolase domain containing 3	3.6
Ramp3	Receptor (calcitonin) activity
	modifying protein 3	3.6
Fibp	Fibroblast growth factor (acidic)
	intracellular binding protein	3.6
Wscr5	Williams-Beuren syndrome chromosome
	region 5 homolog (human)	3.6
Eppk1	Epiplakin 1	3.6
2010004A03Rik	RIKEN cDNA 2010004A03 gene	3.6
Itgb5	Integrin beta 5
	gb: NM_010580 1417534_at	3.5
	gb: NM_010580 1417533_a_at	3.3
Mlf1	Myeloid leukemia factor 1	3.5
Tnfrsf22	Tumor necrosis factor receptor
	superfamily, member 22	3.5
Zdhhc2	Zinc finger, DHHC domain containing 2	3.5
Tnfaip2	Tumor necrosis factor, alpha-induced protein 2	3.4
Rrad	Ras-related associated with diabetes	3.4
A530090O15Rik	RIKEN cDNA A530090O15 gene	3.4
Chi3l4	Chitinase 3-like 4	3.4
Tnfrsf19	Tumor necrosis factor receptor
	superfamily, member 19	3.4
Myo1b	Myosin IB
	gb: AI255256	3.4
	gb: BI080370	3.2
Tuba4	Tubulin, alpha 4	3.3
Myo1g	Myosin IG	3.3
Siat10	Sialyltransferase 10
	(alpha-2,3-sialyltransferase VI)	3.3
Nol3	Nucleolar protein 3
	(apoptosis repressor with CARD domain)	3.3
Tpt1h	tRNA splicing 2’ phosphotransferase 1
	homolog (S. cerevisiae)	3.3
Igfbp6	Insulin-like growth factor binding protein 6	3.3
Ccnd1	Cyclin D1
	gb: M64403	3.2
	gb: NM_007631	3.1
BC003236	cDNA sequence BC003236	3.2
2010001C09Rik	RIKEN cDNA 2010001C09 gene	3.2
Chst1	Carbohydrate (keratan sulfate Gal-6)
	sulfotransferase 1	3.2
Timp1	Tissue inhibitor of metalloproteinase 1	3.2
4921530G04Rik	RIKEN cDNA 4921530G04 gene	3.2
Lxn	Latexin	3.1
Sgk2	Serum/glucocorticoid regulated kinase 2	3.1
2310047E01Rik	RIKEN cDNA 2310047E01 gene	3.1
2200002N01Rik	RIKEN cDNA 2200002N01 gene	3
Ptpre	Protein tyrosine phosphatase, receptor type, E	3
Psmb8	Proteosome (prosome, macropain) subunit, beta
	type 8 (large multifunctional protease 7)	3
Tm7sf1	Transmembrane 7 superfamily member 1	3

Table 2 Differential biological process profile in cell lines Hca-F vs Hca-P.

Development
Itgb5 gb: NM_010580 1417533_a_at 3.3	Ccnd1 gb: M64403	3.2
Mlf1 gb: NM_010580 1417534_at 3.5	gb: NM_007631	3.1
Morphogenesis
Gja1 gb: BC006894	6.4	Sema3b gb: BB116052	5.1
gb:M63801	7.2	gb:NM_009153	4.7
Tnfaip2	3.4	Tm4sf9	3.9
Igfbp6	3.3	Igfbp4 gb: NM_010517	6.3
Egfr gb: AF275367	6.9	gb: AA119124	4
gb: U03425	3.6	gb: BC019836 1423756_s_at 5.8
Efna1 gb: D38146	5.7	gb: BC019836 1423757_x_at 4.1
gb: BC002046	4.2	Eng	4.5
Cellular process
Cell communication
Cell adhesion
Mcam	4.2	Itgb5 gb: NM_010580 1417533_a_at 3.3
Tm4sf9	3.9	gb: NM_010580 1417534_at 3.5
D7Ertd
45 8e gb: BC013673 1423903_at 3.8		Col8a1	4.9
gb: BB049138 1423904_a_at 4	Eng	4.5
gb: BB049138 1423905_at 3.9	Pcdhb7	4.9
gb: NM_009310 4.2
gb: BC013673 1451160_s_at 4
Cell–cell signaling
Gja1 gb: BC006894	6.4
gb: M63801	7.2
Signal transduction
IL2rg gb: L20048 1416295_a_at 3.3	Efna1 gb: BC002046	4.2
gb: L20048 1416296_at 4.3	gb: D38146	5.7
Itgb5 gb: NM_010580 1417533_a_at 3.3	Egfr gb: AF275367	6.9
gb: NM_010580 1417534_at 3.5	gb: U03425	3.6
Dok1	3.6	Fgf15	5.4
Ptpre	3	Cdc42ep5	4.4
Ramp3	3.6	Sh3bp5	5.5
Lepr	6.7	Ptprr	4.1
Eng	4.5	Ripk3	6.4
F2r	4.5	R75183 gb: BC004774	7
Rrad	3.3	gb: BB324973	5.5
Rab3b	5.6
Cellular physiological process
Cell death
Ripk3	6.4	Nol3	3.3
Cell motility
Tm4sf9	3.9	D7Ertd458e gb: BC013673 1423903_at	3.8
Cnn2	5.2	gb: BB049138 1423904_a_at 4
		gb: BB049138 1423905_at 3.9
		gb: NM_009310 4.2
		gb: BC013673 1451160_s_at 4
Cell growth and/or maintenance
Transport
Tuba4	3.3	Slc38a4 gb: NM_027052	9
Ramp3	3.6	gb: AK003626	3.4
Rab3b	5.6	Cav	5.8
Scn8a	4
Cell organization and biogenesis
Igfbp6	3.3	Igfbp4 gb: NM_010517	6.3
Egfr gb: AF275367	6.9	gb: AA119124	4
gb: U03425	3.6	gb: BC019836 1423756_s_at 5.8
AFFX-18SRNAMur	X00686_M_at 5.1	gb: BC019836 1423757_x_at 4.1
Microtubule-based process
Tua4	3.3
Cytoskeleton organization and biogenesis
Krt1-19	7.4	Krt2-8 gb: M21836	8.6
Tuba4	3.3	gb: NM_031170	4.8
Krt2-7	5.2	Myo1b gb: AI255256	3.4
Krt1-18	5.1	gb: BI080370	3.2
Cell proliferation
Tm4sf9	3.9	Pla2g1b	6.4
Cell cycle
Ccnd1 gb: M64403	3.2	Egfr gb: AF275367	6.9
gb: NM_007631	3.1	gb: U03425	3.6
Axl	4
Regulation of cellular process
Igfbp6	3.3	Igfbp4 gb: NM_010517	6.3
Ramp3	3.6	gb: AA119124	4
		gb: BC019836 1423756_s_at 5.8
		gb: BC019836 1423757_x_at 4.1
Cell differentiation
Ccnd1 gb: M64403	3.2	Mlf1	3.5
gb: NM_007631	3.1
Regulation of biological process
Regulation of cellular process
Igfbp6	3.3	Igfbp4 gb: NM_010517	6.3
Ramp3	3.6	gb: BC019836 1423756_s_at 5.8
Sh3bp5	5.5	gb: BC019836 1423757_x_at 4.1
		gb: AA119124	4
Regulation of physiological process
Gja1 gb: BC006894	6.4	Procr	4.6
gb: M63801	7.2
Behavior
Scn8a	4
Nr1d1		4.6
Physiological process
Metabolism
Pla2g1b	6.4	Pla2g7	4.4
Psmb8	3	2310047E01Rik	3.1
Fbp2	7.1	3.3
Protein metabolism/phosphorus metabolism
A530090O15Rik	3.4	Axl	4
Ccnd1 gb: M64403	3.2	Egfr gb: AF275367	6.9
gb: NM_007631	3.1	gb: U03425	3.6
Krt2-8 gb: M21836	8.6	Mak	3.9
gb: NM_031170	4.8	Ptpn8	5.6
Ptpre	3	Ptprr	4.1
Ripk3	6.4	Sgk2	3.1
Nucleobase, nucleoside, nucleotide and nucleic acid metabolism
Nol3	3.3	Lepr	6.7
Transcription
Fosl1 gb: NM_010235	5	Ankrd1 gb: NM_013468	5.3
gb: U34245	4.4	gb: AK009959	3.6
Nfil3	4.6	Nr1d1	4.6
Regulation of physiological process
Gja1 gb: BC006894	6.4	Procr	4.6
gb: M63801	7.2
Coagulation
Procr	4.6	F2r	4.5
Organismal physiological process
Chi3l3	4.1	Chi3l4	3.4
Csf3	4.7	Daf1	5.9
F2r	4.5	Gja1 gb: BC006894	6.4
IL24	5.9	gb: M63801	7.2
Pla2g7	4.4	Procr	4.6
Mus musculus
transcribed sequences	3.8	Psmb8	3
Response to stimulus
Chi3l3	4.1	Chi3l4	3.4
Csf3	4.7	Daf1	5.9
F2r	4.5	IL24	5.9
Gja1 gb: BC006894	6.4	Krt2-8 gb: NM_031170	4.8
gb: M63801	7.2	gb: M21836	8.6
Pla2g1b	6.4	Pla2g7	4.4
Psmb8	3	Serpinh1	4
Mus musculus transcribed sequences	3.8

Table 3 Differential molecular function profile in cell lines Hca-F vs Hca-P.

Transporter activity
Gja1 gb: BC006894	6.4	Slc38a4 gb: AK003626	3.4
gb: M63801	7.2	gb: NM_027052	9
Ramp3	3.6	Rab3b	5.6
Scn8a	4
Tptih	3.3
Structural molecule activity
Eppk1	3.6	Cldn9	7.4
Col8a1	4.9	Krt1-19	7.4
Tuba4	3.3	Krt2-7	5.2
Krt2-8 gb: NM_031170	4.8	Krt1-18	5.1
gb: M21836	8.6
Chaperone activity
Serpinh1	4	Sncg	5
Motor activity
Myo1b gb: BI080370	3.2	Myo1g	3.3
gb: AI255256	3.4
Catalytic activity
Gcnt2	4.2	Siat10	3.3
Chst1	3.2	Loxl2	3.7
Ltb4dh	5.2	2310047E01Rik	3.1
Hydrolase activity
Pla2g1b	6.4	Smpd2	4.3
Abhd3	3.6	Ptpn8	5.6
Ptpre	3	Chi3l3	4.1
Rrad	3.4	Rab3b	5.6
Chi3l4	3.4	Ptprr	4.1
Pla2g7	4.4	Fbp2	7.1
Psmb8	3
Kinase activity
Ccnd1 gb: M64403	3.2	Krt2-8 gb: NM_031170	4.8
gb: NM_007631	3.1	gb: M21836	8.6
A530090O15Rik	3.4
Protein-tyrosine kinase activity
Sgk2	3.1	Egfr gb: AF275367	6.9
Axl	4	gb: U03425	3.6
Ripk3	6.4
Transmembrane receptor protein kinase activity
Egfr gb: AF275367	6.9
gb: U03425	3.6
Protein serine/threonine kinase activity
Sgk2	3.1	Mak	3.9
Axl	4	Egfr gb: AF275367	6.9
Ripk3	6.4	gb: U03425	3.6
Transferase activity
A530090O15Rik	3.4	Axl	4
Ccnd1 gb: M64403	3.2	Egfr gb: AF275367	6.9
gb: NM_007631	3.1	gb: U03425	3.6
Chst1	3.2	Gcnt2	4.2
Krt2-8 gb: NM_031170	4.8	Mak	3.9
gb: M21836	8.6	Ripk3	6.4
Sgk2	3.1	Siat10	3.3
Enzyme regulator activity
Ccnd1 gb: M64403	3.2	Lxn	3.1
gb: NM_007631	3.1	Timp1	3.2
Sh3bp5	5.5	Cd109	5.9
1600023A02Rik	5.3	Serpinh1	4
Binding
Nucleic acid binding
Fosl1 gb: NM_010235	5	Ankrd1 gb: NM_013468	5.3
gb: U34245	4.3	gb: AK009959	3.6
Nr1d1	4.6
Metal ion binding
Pla2g1b	6.4	Smpd2	4.3
Ltb4dh	5.2	Scn8a	4
2310047E01Rik	3.1	Pcdhb7	4.9
2810003C17Rik	4.6	Loxl2	3.7
Zdhhc2	3.5
Nucleotide binding
A530090O15Rik	3.4	Axl	4
Egfr gb: AF275367	6.9	Krt2-8 gb: NM_031170	4.8
gb: U03425	3.6	gb: M21836	8.6
Mak	3.9	Rab3b	5.6
Myo1b gb: BI080370	3.2	Ripk3	6.4
gb: AI255256	3.4	Rrad	3.4
Scn8a	4	Sgk2	3.1
Tuba4	3.3
Receptor binding
Areg	4.3	Csf3	4.7
Dok1	3.6	Fgf15	5.4
Il24	5.9	Pla2g1b	6.4
Protein binding
Ankrd1 gb: NM_013468	5.3	Ccnd1 gb: M64403	3.2
gb: AK009959	3.6	gb: NM_007631	3.1
Cav	5.8	Cdc42ep5	4.4
Col8a1	4.9	Eng	4.5
D7Ertd458e
gb: BC013673 1423903_at 3.8		Egfr gb: AF275367	6.9
gb: BB049138 1423904_a_at 4		gb: U03425	3.6
gb: BB049138 1423905_at 3.9		Fibp	3.6
gb: NM_009310 4.2		IL2rg gb: L20048 1416295_a_at 3.3
gb: BC013673 1451160_s_at 4		gb: L20048 1416296_at 4.3
Itgb5 gb: NM_010580	3.5	Igfbp6	3.3
gb: NM_010580	3.3	Lepr	6.7
Nol3	3.3	Pcdhb7	4.9
Procr	4.6	Ptpre	3
Rab3b	5.6	Rrad	3.4
Sh3bp5	5.5	Tnfrsf22	3.5
Fscn1 gb: NM_007984 1416514_a_at 5.4		Myo1b gb: BI080370	3.2
gb: BE952057	4.2	gb: AI255256	3.4
gb: NM_007984 1448378_at 3.7		Cnn2	5.2
Carbohydrate binding
Chi3l3	4.1	Chi3l4	3.4
Signal transducer activity
Dok1	3.6	Ripk3	6.4
Receptor activity
Axl	4	Itgb5 gb: NM_010580.1	3.5
D7Ertd458e gb: BC013673 1423903_at 3.8		gb: NM_010580.1	3.3
gb: BB049138 1423904_a_at 4		Nr1d1	4.6
gb: BB049138 1423905_at 3.9		Procr	4.6
gb: NM_009310 4.2		Ptpn8	5.6
gb: BC013673 1451160_s_at 4		Ptprr	4.1
Ramp3	3.6	Tnfrsf19	3.4
Tnfrsf22	3.5	Lepr	6.7
IL2rg	gb: L20048.1 1416295_a_at 3.3	Egfr gb: AF275367.1	6.9
gb: L20048.1 1416296_at 4.3		gb: U03425.1	3.6
F2r	4.5

Citation: Song B, Tang JW, Wang B, Cui XN, Hou L, Sun L, Mao LM, Zhou CH, Du Y, Wang LH, Wang HX, Zheng RS, Sun L. Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip. World J Gastroenterol 2005; 11(10): 1463-1472
URL: https://www.wjgnet.com/1007-9327/full/v11/i10/1463.htm
DOI: https://dx.doi.org/10.3748/wjg.v11.i10.1463