Difference of gene expression profiles between esophageal carcinoma and its pericancerous epithelium by gene chip

Table 1 Clinical and pathological data of 11 cases with esophageal carcinoma

No. of in-P	Name	Sex	Age	Pathological diagnosis	Lymph metastasis	Clinical stage
106811	Xu_	F	65	Middle esophageal, marrow type, well-middle d.
				Scc, exterior layer invasion with tumor embolus	0/18	II
106850	Xu _	F	58	Middle esophageal, marrow type, Poor d. Scc with
				Exterior layer invasion	1/8	III
106839	Yu _	M	60	Middle-inferior esophageal, marrow type, well-middle d.
				Scc, exterior layer invasion with tumor embolus	0/26	II
107001	Zhou _	M	53	Middle esophageal, ulcer type, middle d. Scc,
				Exterior layer invasion with tumor embolus	4/19	III
107151	Wang_	M	42	Middle-up esophageal, marrow type, middle d.
				Scc with exterior layer invasion	0/8	II
107326	Gu _	M	51	Middle- inferior esophageal, marrow type,
				Middle-Poor d. Scc with exterior layer invasion	2/14	III
107546	Zhao_	F	63	Middle- inferior esophageal, ulcer type, well-
				Middle d. Scc with shallow muscle layer invasion	0/15	II
107564	Lu_	M	61	Middle- inferior esophageal, marrow type,
				Middle d. Scc with deep muscle layer invasion	1/32	III
107146	Chen_	F	65	Superior esophageal, ulcer type, well d.
				Scc with exterior layer invasion	0/17	II
107527	Xu_	M	49	Inferior esophageal, ulcer type, middle d.
				Scc with shallow muscle layer invasion	1/18	III
107531	Guan_	M	56	Middle esophageal, marrow type, middle d.
				Scc with deep muscle layer invasion	0/26	II

d.: differentiated Scc: squamous cell carcinoma.

Table 2 Genes with expression difference > 3 or < 0.33 on average ratio between esophageal carcinoma and normal epithelium

Genbank-ID	Fcf	Gene name	R1	R2	AR
hsu67963		Human lysophospholipase homolog(HU-K5)mRNA, complete cds.	0.11	0.16	0.14
Hslimdp	8	H.sapiens mRNA for ZNF185 gene.	0.15	0.23	0.19
4505166			0.13	0.26	0.19
d87451	15	Human mRNA for KIAA0262gene,complete cds	0.13	0.31	0.22
hsy15409	11	Homo sapiens mRNA for putative glucose 6-phosphate translocase.	0.28	0.23	0.25
hsu16996	12	Human protein tyrosine phosphatase mRNA, complete cds.	0.31	0.26	0.29
hsu30255	12	Human phosphogluconate dehydrogenase (hPGDH) gene, complete cds.	0.29	0.30	0.29
4504714			0.47	0.16	0.31
ab002349	15	Human mRNA for KIAA0351 gene, complete cds.	0.14	0.50	0.32
humpai2	13	Human placental plasminogen activator inhibitor mRNA, complete cds.	0.28	0.35	0.32
hsu73824		Human p97 mRNA, complete cds.	0.30	0.34	0.32
hsa132270	2	Homo sapiens mRNA for integral type I protein p24B (p26).	0.31	0.34	0.33
Humorfkg1f	11	Human mRNA for KIAA0058 gene,complete cds.	0.31	0.36	0.33
s74452	3	Cyclin B1{promoter region}[human,cervical carcinoma cell line, HeLa cells,Genomic, 351 nt].	3.21	2.79	3.00
hspros27	10	H.sapiens PROS-27 mRNA.	3.29	2.85	3.07
Hstrr	10	Human mRNA for transferrin receptor.	2.70	3.48	3.09
Humprion	15	Homo sapiens mRNA for prion protein, complete cds.	3.07	3.19	3.13
hshr21spa	13	H.sapiens mRNA for protein involved in DNA double-strand break repair.	2.29	4.01	3.15
AB00109S14	11	Homo sapiens gene for H-cadherin, exon 14 and complete cds.	2.95	3.50	3.23
hsranbp1	11	H.sapiens mRNA for RanBP1.	3.98	2.57	3.27
Hsxprf	8	Homo sapiens mRNA for putative transcription factor XPRF.	3.35	3.38	3.37
humcd3621	11	Human antigen CD36 (clone 21) mRNA, complete cds.	3.28	3.54	3.41
Humsparc	5	Human SPARC/osteonectin mRNA, complete cds.	2.87	3.96	3.42
Humhcamap3	5	Human gene for hepatitis C-associated microtubular aggregate protein p44, exon 4.	3.72	3.30	3.51
Humprofii	5	Human profilin II mRNA, complete cds.	3.07	4.07	3.57
5729755			2.35	4.88	3.61
Hsrnasmg	13	H.sapiens mRNA for Sm protein G.	2.91	4.57	3.74
Humpgc	5	Human chondroitin sulfate proteoglycan core protein mRNA, 3' end.	3.67	3.91	3.79
hstop2a10	8	Homo sapiens topoisomerase II alpha (TOP2A) gene,exons 34 and 35,and complete cds.	4.02	3.76	3.89
hsu09559	14	Human Rch1 (RCH1) mRNA, complete cds.	3.75	4.03	3.89
humcol1a42		Human alpha-1 collagen type IV gene, exon 52.	4.37	3.69	4.03
hsinta6r	11	Human mRNA for integrin alpha 6.	3.28	5.43	4.35
d86983	15	Human mRNA for KIAA0230 gene, partial cds.	4.71	4.84	4.78
hsu26555		Human versican V2 core protein precursor splice-variant mRNA, complete cds.	6.93	5.91	6.42
hspgp95	13	Human mRNA for protein gene product (PGP) 9.5.	5.66	7.54	6.60
af052124	15	Homo sapiens clone 23810 osteopontin mRNA, complete cds.	11.77	4.63	8.20
Humcolva		Human alpha-2 type V collagen gene, 3' end.	7.64	10.17	8.91
humca1xia	15	Human alpha-1 type XI collagen (COL11A1) mRNA, complete cds.	6.75	12.07	9.41
Hscalbr11		Human mRNA for 27-kDa calbindin.	6.72	12.17	9.45
hsu50078	8	Human guanine nucleotide exchange factor p532 mRNA, complete cds.	12.28	17.11	14.70
Hsop	5	Human mRNA for osteopontin.	20.23	20.22	20.23

Fcf: function classification average ratio > 3: up regulation average ratio < 0.33: down regulation; R1: the first ratio; R2: the second ratio; AR: R1 + R2 average ratio.

Table 3 Function classification for genes showing expression differences in esophageal carcinoma and pericancerous epithelium that were > 2 or < 0.5 fold from the control tissue

	Gene function classification	Carcinoma/normal			Pericancerous/normal
		N	> 2	< 0.5	N	> 2	< 0.5
1	Proto-oncogenes and tumor suppression genes	2	1	1	0	0	0
2	Cell signals and transducing proteins	3	2	1	3	3	0
3	Cell cycle proteins	6	5	1	0	0	0
4	Extra-pressure reaction proteins	1	0	1	0	0	0
5	Cell regulatory proteins	7	7	0	3	3	0
6	Cell apoptosis related proteins	1	1	0	1	0	1
7	DNA synthesis, repair and recombinant proteins	3	3	0	0	0	0
8	DNA binding, transcription and its factor	6	4	2	1	1	0
9	Cell receptors	0	0	0	0	0	0
10	Cell surface antigen and adhesion proteins	10	8	2	4	4	0
11	Ion-channel and transporters	24	14	10	2	2	0
12	Metabolism-related proteins	21	10	11	6	4	2
13	Protein synthesis-related genes	14	7	7	2	1	1
14	Development-related genes	1	1	0	2	2	0
15	Other genes	27	18	9	7	7	0
16	New genes	9	4	5	0	0	0
Total		135	85	50	31	27	4

Table 4 Genes showing expression difference between the esophageal carcinoma and pericancerous epithelium

Genbank-ID	Fcf	Gene name	PR	TR
Hscalbr	11	Human mRNA for 27-kDa calbindin.	2.91	9.45
af052124	15	Homo sapiens clone 23810 osteopontin mRNA, complete cds.	5.34	8.20
Hsinta6r	11	Human mRNA for integrin alpha 6.	2.93	4.35
Humprofii	5	Human profilin II mRNA, complete cds.	2.50	3.57
Humhcamap3	5	Human gene for hepatitis C-associated microtubular aggregate protein p44, exon 4.	2.79	3.51
hum927a	10	Human interferon-inducible protein 9-27 mRNA, complete cds.	2.43	2.92
Hstrr	10	Human mRNA for transferrin receptor.	3.76	3.09
hsu50078	8	Human guanine nucleotide exchange factor p532 mRNA, complete cds.	18.7	14.7
Humtfrr	10	Human transferrin receptor mRNA, complete cds.	3.51	2.81
hsu30255	12	Human phosphogluconate dehydrogenase(hPGDH)gene, complete cds.	0.48	0.29
hsu05684	2	Homo sapiens dihydrodiol dehydrogenase mRNA, complete cds.	3.75	2.31
Hsop	5	Human mRNA for osteopontin.	37.1	20.2
Hspgp95	13	Human mRNA for protein gene product (PGP) 9.5.	19.4	6.60
hsu46571	13	Human tetratricopeptide repeat protein (tpr2) mRNA, complete cds.	0.41
Humrsc390	6	Human mRNA for KIAA0018gene, complete cds.	0.44
hcox4gn	12	Homo sapiens hypothetical protein (COX4AL) gene, partial cds, and cytochromec oxidase subunit IV precursor (COX4) gene, complete cds.	0.47
d79997		Human mRNA for KIAA0175 gene, complete cds.	2.05
ab01755s10	15	Homo sapiens IGSF4 gene, exon 10 and complete cds.	2.06
Hsnov	15	H.sapiens mRNA for novel gene in Xq28 region.	2.09
hsifi56r		Human mRNA for 56-KDa protein induced by interferon.	2.1
af054182	12	Homo sapiens mitochondrial processing peptidase beta-subunit mRNA, complete cds.	2.11
af131818	15	Homo sapiens clone 25237mRNA sequence.	2.19
af035301	2	Homo sapiens clone 23876 neuronal olfactomedin-related ER localized protein mRNA, partial cds.	2.28
Humorfi	14	Homo sapiens (clone S240ii117/zap112) mRNA, complete cds.	2.26
af038660	12	Homo sapiens chromosome 1p33-p34 beta-1,4-galactosyltransferase mRNA, complete cds.	2.32
d88687	12	Homo sapiens mRNA for KM-102-derived reductase-like factor,complete cds.	2.51
hsu05598	12	Human dihydrodiol dehydrogenase mRNA, complete cds.	3.07
Humalcam	10	Homo sapiens CD6 ligand (ALCAM) mRNA, complete cds.	3.07
hsu79299	2	Human neuronal olfactomedin-related ER localized protein mRNA,partial cds.	3.33
ab003476	14	Homo sapiens mRNA for gravin, complete cds. 3.65
af100757	15	Homo sapiens COP9 complex subunit 4 mRNA, complete cds. 5.96

Fcf: function classification; TR: esophageal carcinoma average ratio; PR: pericancerous epithelium average ratio.