Identification of Hub Genes Associated with Gastric Cancer via Bioinformatics Analysis and Validation Studies

Figures & data

Figure 1 Volcano plots and heatmaps of DEGs. (A) Volcano plot of DEGs in GSE33335 dataset. (B) Heatmap of DEGs in GSE33335 dataset. (C) Volcano plot of DEGs in GSE79973 dataset. (D) Heatmap of DEGs in GSE79973 dataset. (E) Volcano plot of DEGs in TCGA data. (F) Heatmap of DEGs in TCGA data. (G) Venn diagram of DEGs.

Abbreviations: DEG, differentially expressed genes; TCGA, The Cancer Genome Atlas.

Figure 2 The GO and KEGG functional enrichment analyses of overlapping DEGs in gastric cancer. (A) The GO term, biological processes of common DEGs. (B) The GO term, cellular composition of common DEGs. (C) The GO term, molecular function of common DEGs. (D) KEGG pathway enrichment analyses of common DEGs.

Abbreviations: GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; DEG, differentially expressed genes.

Figure 3 Protein interaction network diagram of common DEGs and identifying of hub genes. (A) The protein interaction network diagram of the common DEGs using online analysis tool STRING. (B) The ranking column chart of the hub genes by R software (top 30 genes).

Abbreviation: DEG, differentially expressed genes.

Figure 4 Validation of selected hub genes expression in gastric cancer tissues and normal tissues using GEPIA database. ((A–J): COL1A1, COL3A1, COL1A2, CCNB1, COL4A1, SERPINH1, SPARC, MAD2L1, BGN and CDKN3). *P < 0.05.

Figure 5 The validation of prognostic value of 10 genes. ((A–J): COL1A1, COL3A1, COL1A2, CCNB1, COL4A1, SERPINH1, SPARC, MAD2L1, BGN and CDKN3).

Figure 6 Correlation between the expression of prognostic genes and clinicopathological features of GC (Ualcan database). (A) The expression of 2 prognosis-related genes in GC. (B) Correlation between expression of 4 prognosis-related genes and tumor stages in GC patients. (C) Expression of 2 prognosis-related genes in GC based on nodal metastasis status. (D) Expression of 2 prognosis-related genes in GC based on tumor grades. *P < 0.05, ***P < 0.001.

Abbreviation: GC, gastric cancer.

Figure 7 The immunohistochemical-based protein expression of 2 prognosis-related genes in GC tissues and adjacent normal tissues.

Abbreviation: GC, gastric cancer.

Table 1 Relationship Between Prognosis-Related Genes and Clinicopathological Features in Patients with GC

Variables	Cases	COL1A1 Expression		χ^2	P	COL4A1 Expression		χ^2	P
		+	−			+	−
Gender
Male	49	37	12	1.333	0.248	37	12	0.581	0.446
Female	21	13	8			14	7
Age (years)
≤61	32	21	11	0.973	0.324	19	13	5.418	0.020
>62	38	29	9			32	6
Tumor location
Upper 1/3	18	12	6	2.087	0.581	11	7	2.543	0.480
Middle 1/3	15	9	6			11	4
Lower 1/3	31	24	7			25	6
Whole stomach	6	5	1			4	2
Infiltrating depth
T1	9	3	6	9.842	0.012	4	5	5.211	0.137
T2	11	6	5			7	4
T3	43	35	8			34	9
T4	7	6	1			6	1
Lymph node metastasis
N0	28	20	8	2.516	0.484	16	12	12.01	0.005
N1	16	13	3			11	5
N2	8	4	4			6	2
N3	18	13	5			18	0
Clinical stage
I	15	7	8	5.743	0.046	7	8	8.903	0.012
II	27	20	7			19	8
III	28	23	5			25	3
Differentiation degree
Well-Moderately	46	29	17	4.622	0.032	32	14	0.735	0.391
Poorly	24	21	3			19	5
Lauren classification
Intestinal type	26	17	9	0.835	0.700	18	8	1.397	0.570
Diffuse type	14	11	3			12	2
Mixed type	30	22	8			21	9

Table 2 Relationship Between 5-Year Survival Rate and Clinicopathological Features in Patients with GC

Variables	Cases	5-Year Survival Rate	χ^2	P
Gender
Male	49	53.06%(26/49)	0.099	0.753
Female	21	57.14%(12/21)
Age (years)
≤61	32	53.13%(17/32)	0.032	0.858
>62	38	55.26%(21/38)
Tumor location
Upper 1/3	18	44.44%(8/18)	0.931	0.818
Middle 1/3	15	53.33%(8/15)
Lower 1/3	31	51.61%(16/31)
Whole stomach	6	66.66%(4/6)
Infiltrating depth
T1	9	100%(9/9)	14.14	0.003
T2	11	72.73%(8/11)
T3	43	48.83%(21/43)
T4	7	14.29%(1/7)
Lymph node metastasis
N0	28	75.00%(21/28)	10.34	0.016
N1	16	62.50%(10/16)
N2	8	50.00%(4/8)
N3	18	27.78%(5/18)
Clinical stage
I	15	86.67%(13/15)	11.63	0.003
II	27	51.85%(14/27)
III	28	32.14%(9/28)
Differentiation degree
Well-Moderately	46	73.91%(34/46)	5.416	0.020
Poorly	24	45.83%(11/24)
Lauren classification
Intestinal type	26	57.69%(15/26)	0.927	0.629
Diffuse type	14	42.86%(6/14)
Mixed type	30	56.67%(17/30)
COL1A1 expression
Low	20	75.00%(15/20)	6.228	0.013
High	50	42.00%(21/50)
COL4A1 expression
Low	19	68.42%(14/19)	7.372	0.007
High	51	37.25%(19/51)

Figure 8 Relationship between prognosis-related genes expression level and 5-year survival rate of patients with GC (n=70). (A) Relationship between COL1A1 expression level and 5-year survival rate of patients with GC. (B) Relationship between COL4A1 expression level and 5-year survival rate of patients with GC.

Abbreviation: GC, gastric cancer.