Differential gene expression profiling of gastric intraepithelial neoplasia and early-stage adenocarcinoma

Table 1 Clinical characteristics of all patients

	Discovery phase(n = 77)	Validation phase(n = 75)	P value
Gender			0.48
Male	46	49
Female	31	26
Age (yr)			0.14
Mean ± SE (range)	58.87 ± 9.13 (36-78)	56.61 ± 9.39 (36-79)

Table 2 Clinicopathological characteristics of early-stage gastric carcinoma

	Discovery phase(n = 19)	Validation phase(n = 14)	P value
Depth of invasion			0.31
Tunica mucosa	6	2
Muscularis mucosae	8	5
Submucosa	5	7
Differentiation			0.56
Well	5	4
Moderate	4	5
Poor	10	5

Table 3 Enriched Gene Ontology terms of the upregulated transcripts in high-grade intraepithelial neoplasia compared with low-grade intraepithelial neoplasia

GO accession	GO term	P value	Genes involved
GO:0043170|GO:0043283	Macromolecule metabolic process	4.01 × 10-9	272
GO:0044260|GO:0034960	Cellular macromolecule metabolic process	3.84 × 10-9	247
GO:0006952|GO:0002217|GO:0042829	Defense response	9.44 × 10-8	63
GO:0005515|GO:0045308	Protein binding	1.09 × 10-7	358
GO:0044422	Organelle part	3.35 × 10-7	292
GO:0044428	Nuclear part	4.51 × 10-7	145
GO:0044446	Intracellular organelle part	4.17 × 10-7	288
GO:0070013	Intracellular organelle lumen	5.50 × 10-6	144
GO:0043122	Regulation of I-κB kinase/NF-κB cascade	6.79 × 10-6	21
GO:0043123	Positive regulation of I-κB kinase/NF-κB cascade	9.53 × 10-6	18

NF-κB: Nuclear factor-κB; GO: Gene ontology.

Table 4 Enriched Gene Ontology categories of the upregulated transcripts in early-stage gastric carcinoma compared with high-grade intraepithelial neoplasia

GO accession	GO term	P value	Genes involved
GO:0050776	Regulation of the immune response	2.27 × 10-8	9
GO:0050851	Antigen receptor-mediated signaling pathway	4.24 × 10-7	5
GO:0002429	Immune response-activating cell surface receptor signaling pathway	5.82 × 10-7	5
GO:0050863	Regulation of T cell activation	6.90 × 10-7	6
GO:0002768	Immune response-regulating cell surface receptor signaling pathway	7.10 × 10-7	5
GO:0050778	Positive regulation of the immune response	3.23 × 10-7	7
GO:0002684	Positive regulation of the immune system process	3.92 × 10-7	8
GO:0001772	Immunological synapse	1.95 × 10-6	3
GO:0051249	Regulation of lymphocyte activation	2.53 × 10-6	6
GO:0042102	Positive regulation of T cell proliferation	2.81 × 10-6	4

GO: Gene ontology.

Table 5 Statistical results of the differential expression of G₀S₂ among tissue samples in the microarray data

Unpaired t-test of G0S2	P value (corr)	P value	FC (abs)	Direction	Probe name	Gene symbol description
HGIN vs LGIN	0.021	0.001	3.28	Up in HGIN	A_23_P74609	Homo sapiens G0/G1 switch 2 (G0S2), mRNA NM_015714
EGC vs LGIN	< 0.001	< 0.001	6.00	Up in EGC
HGIN vs Gastritis	0.005	0.001	3.19	Up in HGIN
EGC vs Gastritis	< 0.001	< 0.001	5.83	Up in EGC
EGC vs HGIN	0.463	0.103	1.83	Up in EGC
LGIN vs Gastritis	0.946	0.927	1.03	Down in LGIN

HGIN: High-grade intraepithelial neoplasia; EGC: Early-stage adenocarcinoma; LGIN: Low-grade intraepithelial neoplasia.

Table 6 Statistical results of the differential expression of G₀S₂ among tissue samples in immunohistochemical staining data n (%)

	G0S2 < 5(n = 131)	G0S2≥ 5(n = 24)	Pearson χ2 of4 groups
Gastritis (n = 61)1-3	61 (100.0)	0 (0)	P < 0.001
LGIN (n = 24)	21 (87.5)	3 (12.5)
HGIN (n = 40)45	23 (57.5)	17 (42.5)
EGC (n = 30)	26 (86.7)	4 (13.3)

¹Compared with low-grade intraepithelial neoplasia (LGIN), P = 0.005;

²Compared with HGIN, P < 0.001; ³Compared with EGC, P = 0.004;

⁴Compared with LGIN, P = 0.012;

⁵Compared with EGC, P = 0.008. HGIN: High-grade intraepithelial neoplasia; EGC: Early-stage adenocarcinoma.