Gene expression profile differences in gastric cancer, pericancerous epithelium and normal gastric mucosa by gene chip

Table 1 Clinical and pathological data of five patients with gastric cancer.

Number of In-P	Name	Sex	Age (yr)	Pathological diagnosis	Lymph metastasis	Clinical stage
113702	Jiang	F	45	Lesser curvature of stomach invasion ulcer type moderate differentiation adenocarcinoma invasion serosa	1/35	III
123730	Xu	M	48	Anterior wall in body of stomach moderate differentiation adenocarcinoma invasion muscular layers and nerve	1/17	III
123673	Tang	F	57	Lesser curvature in cardia of stomach invasion ulcer type moderate differentiation adenocarcinoma invasion serosa	1/14	III
123808	Yu	F	49	Anterior wall in cardia of stomach poor-moderate differentiation adenocarcinoma, a part of mucinous adenocarcinoma and esophagus of extremities inferior	0/35	II
123733	Huang	M	60	Cardia of stomach node type moderate differentiation adenocarcinoma invasion muscular layer esophagus	5/22	III

Table 2 Differentially expressed gene number in T, P and C.

Numbers of genes	Up-regulated		Down-regulated
	SLR>2	SLR>3	SLR <-2	SLR <-3
T vs C	530	157	236	113
P vs C	50	17	14	7
T and P vs C	108	21	35	17

Table 3 Up-regulated and down-regulated genes.

Probe Set ID	T vs C SLR	P vs C SLR	Name	GO molecular function
202580-x-at	2	2.4	Forkhead box M1	GO:3702; RNA polymerase II transcription factor activity; traceable author statement
				GO:3700; transcription factor activity; traceable author statement
203098-at	2.3	2.4	Chromodomain protein, Y chromosome-like	GO:3682; chromatin binding; inferred from electronic annotation
				GO:3824; enzyme activity; inferred from electronic annotation
203334-at	3.1	3.8	DEAD/H (Asp-Glu-Ala-Asp/His)	GO:3723; RNA binding; inferred from electronic annotation box polypeptide 8 (RNA helicase)
				GO:8248; pre-mRNA splicing factor activity; traceable author statement
				GO:5524; ATP binding; inferred from electronic annotation
				GO:4004; ATP dependent RNA helicase activity; traceable author statement
208152-s-at	1.9	2.1	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21	GO:3723; RNA binding; inferred from electronic annotation
				GO:5524; ATP binding; inferred from electronic annotation
				GO:4004; ATP dependent RNA helicase activity; traceable authorstatemen
209820-s-at	2.2	2.3	Transducin (beta)-like 3	GO:5057; receptor signaling protein activity; predicted/computed
217173-s-at	3.4	3.6	Low density lipoprotein receptor (familial hypercholesterolemia)	GO:5041; low-density lipoprotein receptor activity; traceable author statement
				GO:5509; calcium ion binding; inferred from electronic annotation
				GO:8034; lipoprotein binding; traceable author statement
				GO:5319; lipid transporter activity; inferred from electronic
207102-at	-2.4	-3.6	Aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase)	GO:5489; electron transporter activity; experimental evidence
208580-x-at	-2.7	-3	H4 histone family, member E (H4FE)	Unknown
218730-s-at	-2.5	-3.3	Osteoglycin (osteoinductive factor, mimecan)	GO:8083; growth factor activity; inferred from electronic annotation

Table 4 Comparison between gene molecular functions of T, P and C.

Molecular function	Up-regulated (SLR> 2)	Down-regulated (SLR <-2)
Enzyme activity	15	4
Enzyme regular activity	4	0
Structural molecule activity	3	1
Transcription factor activity	3	0
Nucleic acid binding (RNA, DNA)	16	5
Protein binding activity (Ca , GF, cell skeleton)	14	7
Carbohydrate binding activity	3	0
Metal ion binding activity	1	0
Signal transduction activity (receptor, GF)	7	3
Sport activity	2	1
Transporter activity (electron, ion, protein)	7	6
Tumor antigen	2	0
Tumor suppressor	3	0
Apoptosis suppressor	1	0
Fibrinogen	0	1
Unknown	27	7
Total	108	35

Table 5 Comparison between molecular functions of 21 genes in T, P and C.

Probe Set ID	T vs C SLR	P vs C SLR	Name	GO molecular function
201655-s-at	3.1	2.6	Heparan sulfate	GO:5198; structural molecule activity; inferred from electronic annotation
			proteoglycan 2 (perlecan)	GO:5206; heparin sulfate proteoglycan; traceable author statement
201890-at	3.1	1.6	Ribonucleotide reductase	GO:4748; ribonucleoside-diphosphate reductase activity;non-traceable
			M2 polypeptide	author statement
				GO:16491; oxidoreductase activity; inferred from electronic annotation
201926-s-at	3.1	1	Decay accelerating factor for complement (CD55, Cromer blood group system)	Unknown
203334-at	3.1	3.8	DEAD/H (Asp-Glu-Ala—Asp/His) box polypeptide 8(RNA helicase)	GO:3723; RNA binding; inferred from electronic annotation
				GO:8248; pre-mRNA splicing factor activity; traceable author statement
				GO:5524; ATP binding;inferred from electronic annotation
				GO:4004; ATP dependent RNA helicase activity; traceable author statement
202870-s-at	3.3	1.5	CDC20 cell division cycle 20 homolog (S. cerevisiae)	Unknown
209035-at	3.3	1.6	Midkine (neurite growth- promoting factor 2)	GO:8201; heparin binding; not recorded
				GO:8083; growth factor activity; not recorded
				GO:5125; cytokine activity; not recorded
209803-s-at	3.4	1.8	Tumor suppressing subtransferable candidate 3	Unknown
212444-at	3.4	1.2	Homo sapiens, clone IMAGE:4471726, mRNA	Unknown
217173-s-at	3.4	3.6	Low density lipoprotein receptor (familial hypercholesterolemia)	GO:5041; low-density lipoprotein receptor activity; traceable author statement
				GO:5509; calcium ion binding; inferred from electronic annotation
				GO:8034; lipoprotein binding; traceable author statement
				GO:5319; lipid transporter activity; inferred from electronic
217221-x-at	3.5	2.2	RNA binding motif protein 10	GO:3676; rrm; nucleic acid binding activity; 8.4e-05; extended: inferred from electronic annotation
				GO:3676; rrm; nucleic acid binding activity; 0.76; extended: inferred from electronic annotation
202855-s-at	3.6	1.2	Solute carrier family 16 (monocarboxylic acid transporters), member 3	GO:8028; monocarboxylic acid transporter activity; traceable author statement
				GO:15355; monocarboxylate porter activity; inferred from electronic annotation
				GO:15293; symporter activity; inferred from electronic annotation
203559-s-at	3.6	1.2	Amiloride binding protein 1(amine oxidase (copper-containing))	GO:8144; drug binding;not recorded
				GO:8201; heparin binding; inferred from electronic annotation
				GO:8122; amine oxidase (copper-containing) activity; inferred from electronic annotation
				GO:16491; oxidoreductase activity; inferred from electronic annotation
209373-at	3.8	1.6	BENE protein	Unknown
203108-at	4.2	1.5	Retinoic acid induced 3	GO:8067; metabotropic glutamate, GABA-B-like receptor activity; inferred from electronic annotation
				GO:4872; receptor activity; inferred from electronic annotation
202067-s-at	4.5	3.8	Low density lipoprotein receptor (familial hypercholesterolemia)	GO:5041; low-density lipoprotein receptor activity; traceable author statement
				GO:5509; calcium ion binding; inferred from electronic annotation
				GO:8034; lipoprotein binding; traceable author statement
				GO:5319; lipid transporter activity; inferred from electronic
218900-at	4.5	3.7	Cyclin M4	Unknown
201884-at	4.6	2.1	Carcinoembryonic antigen-related cell adhesion molecule 5	GO:8222; tumor antigen; traceable author statement
211657-at	5.9	2.1	Carcinoembryonic antigen- related cell adhesion molecule 6	GO:8222; tumor antigen; traceable author statement
212768-s-at	4.7	1.3	Differentially expressed in hematopoietic lineages	Unknown
208250-s-at	6.3	1.7	Deleted in malignant brain tumors 1	GO:8181; tumor suppressor; predicted/computed
				GO:5044; SRCR; scavenger receptor activity; 3.7e-42;extended: unknown
204855-at	7.7	4.2	Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin) member 5	GO:4868; serpin; not recorded GO:4867; serine protease nhibitor activity; inferred from electronic annotation
				GO:8181; tumor suppressor; traceable author statement serp

Table 6 Comparison between molecular functions of 17 genes in T, P and C.

Probe Set ID	T vs C SLR	P vs C SLR	Name	GO molecular function
207102-at	-2.4	-3.6	Aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5- beta-reductase)	GO:5489; electron transporter activity; experimental evidence
218730-s-at	-2.5	-3.3	Osteoglycin (osteoinductive factor, mimecan)	GO:8083; growth factor activity; inferred from electronic annotation
204940-at	-3.3	-1.3	Phospholamban	GO:42030; ATPase inhibitor activity; inferred from electronic annotation
				GO:5246; calcium channel regulator activity; not recorded
208281-x-at	-3.3	-1.1	Deleted in azoospermia 3	GO:3676; nucleic acid binding; inferred from electronic annotation
216351-x-at	-3.3	-1.6	Deleted in azoospermia 4	Unknown
209894-at	-3.7	-1.5	Leptin receptor	GO:4896; hematopoietin/interferon-class (D200-domain) cytokine receptor activity; inferred from electronic annotation
214723-x-at	-3.7	-1.5	KIAA1641 protein	Unknown
208282-x-at	-4.3	-1.2	Deleted in azoospermia 2	GO:3676; nucleic acid binding; inferred from electronic annotation
219564-at	-4.3	-1.2	Potassium inwardly- rectifying channel, subfamily J, member 16	GO:5242; inward rectifier potassium channel activity; inferred from electronic annotation
				GO:5244; voltage-gated ion channel activity; inferred from electronic annotation
				GO:5267; potassium channel activity; inferred from electronic annotation
203571-s-at	-4.8	-1.6	Adipose specific 2	Unknown
218087-s-at	-5	-1.3	Sorbin and SH3 domain containing 1	GO:8092; cytoskeletal protein binding; experimental evidence
				GO:3779; actin binding; experimental evidence
207909-x-at	-5.2	-1.2	Deleted in azoospermia	GO:3676; rrm; nucleic acid binding activity; 4.3e-10; extended: inferred from electronic annotation
				GO:3723; RNA binding; predicted/computed
213071-at	-5.3	-1.3	Dermatopontin	GO:5515; protein binding; traceable author statement
				GO:5194; cell adhesion molecule activity; inferred from electronic annotation
201497-x-at	-5.4	-1	Myosin, heavy polypeptide 11, smooth muscle	GO:3779; actin binding; inferred from electronic annotation
				GO:5516; calmodulin binding; inferred from electronic annotatio
				GO:5524; ATP binding; inferred from electronic annotation
				GO:3774; motor activity; inferred from electronic annotation
207912-s-at	-5.9	-1.3	Deleted in azoospermia	GO:3676; rrm; nucleic acid binding activity; 4.3e-10;extended:inferred from electronic annotation
				GO:3723; RNA binding;predicted/computed
220630-s-at	-6.3	-1.8	Eosinophil chemotactic cytokine	GO:16787; Glyco_hydro_18; hydrolase activity; 2.7e-81; extended:Unknown
				GO:16798; hydrolase activity, acting on glycosyl bonds;inferred from electronic annotation
				GO:8061; chitin binding;inferred from electronic annotation
				GO:8843; endochitinase activity; inferred from electronic annotation
209612-s-at	-6.9	-1.4	Alcohol dehydrogenase IB (class I), beta polypeptide	GO:4024; alcohol dehydrogenase activity, zinc-dependent;traceable author statement
				GO:4327; 1.2.1.1; formaldehyde dehydrogenase (glutathione) activity; 3.69e-120; extended: inferred from electronic annotation
				GO:4023; alcohol dehydrogenase activity, metal ion- independent; inferred from electronic annotation
				GO:4025; alcohol dehydrogenase activity, iron-dependent;inferred from electronic annotation
				GO:8270; zinc ion binding; traceable author statement
				GO:4552; 1.1.1.73; octanol dehydrogenase activity; 4.76e-120; extended: non-traceable author statement
				GO:16491; oxidoreductase activity; inferred from electronic annotation
				GO: 5489; electron transporter activity; traceable author statement