Identification of key genes and pathways in gastric signet ring cell carcinoma based on transcriptome analysis

Table 1 Primers used for quantitative real-time polymerase chain reaction

Gene	Primer sequence (5’-3’)
MAGEA2/3/6; primer 1	F: CAGAGGAGTCAGCACTGCAA
	R: TAGTCGAGAAGCTGGAGGCT
MAGEA2/3/6; primer 2	F: CAGAGGAGTCAGCACTGCAA
	R: TAGTCGAGAAGCTGGAGGCT
MAGEA4	F: CTGCTGTCTCCTCCTCCTCT
	R: GGAACAAGGACTCTGCGTCA
MAGEA2/3/6; primer 3	F:CAGAGGAGTCAGCACTGCAA
	R:GACTCTGGGGAGGATCTGGT
REG1A	F: TGACCCCAAAAAGAACCGCC
	R: AGAACTTGTCTTCACAAGGCAC
REG1B	F: GATCCCCGAGCAGTGCTAAT
	R: CTTCTCACAAGATTCATCCTTCCA
GAPDH	F: TGTTGCCATCAATGACCCCTT
	R: CTCCACGACGTACTCAGCG

F: Forward; R: Reverse.

Table 2 Characteristics of 30 gastric signet ring cell carcinoma and 30 adenocarcinoma patients, n (%)

Characteristic	Overall (n = 60)	GSRCC (n = 30)	Adenocarcinoma (n = 30)	P value
Age (yr)				0.052
≤ 65	41 (68.3)	24 (80.0)	17 (56.7)
> 65	19 (31.7)	6 (20.0)	13 (43.3)
Gender				0.584
Male	40 (66.7)	21 (70.0)	19 (63.3)
Female	20 (33.3)	9 (30.0)	11 (36.7)
Tumor size (cm)				0.584
≤ 5	40 (66.7)	21 (70.0)	19 (63.3)
> 5	20 (33.3)	9 (30.0)	11 (36.7)
Lauren type				0
Intestinal	12 (20.0)	0 (0)	12 (40.0)
Diffuse	35 (58.3)	26 (86.7)	9 (30.0)
Mixed	12 (20.0)	4 (13.3)	8 (26.7)
Unknown	1 (1.67)	0 (0)	1 (3.3)
Histology differentiation				0.038
Poorly/un-differentiated	56 (93.3)	30 (100.0)	26 (86.7)
Well/moderately differentiated	4 (6.7)	0 (0)	4 (13.3)
Unknown
T stage				0.725
T1	5 (8.3)	3 (10.0)	2 (6.7)
T2	9 (15.0)	3 (10.0)	6 (20.0)
T3	12 (20.0)	6 (20.0)	6 (20.0)
T4	34 (56.7)	18 (60.0)	16 (53.3)
N stage				0.639
N0	16 (26.7)	8 (26.7)	8 (26.7)
N1	6 (10.0)	3 (10.0)	3 (10.0)
N2	20 (33.3)	8 (26.7)	12 (40.0)
N3	18 (30.0)	11 (36.7)	7 (23.3)
M stage				0.15
Metastasis	2 (3.3)	2 (6.7)	0 (0)
No metastasis	58 (96.7)	28 (93.3)	30 (100.0)
Positive lymph nodes				0.39
≤ 8	43 (71.7)	20 (66.7)	23 (76.7)
> 8	17 (28.3)	10 (33.3)	7 (23.3)
Lymphovascular invasion				0.355
Yes	31 (51.7)	15 (50.0)	16 (53.3)
No	27 (45.0)	13 (43.3)	14 (46.7)
Unknown	2 (3.3)	2 (6.7)	0 (0)
Nerve invasion				0.213
Yes	42 (70.0)	22 (73.3)	20 (66.7)
No	16 (26.7)	6 (20)	10 (33.3)
Unknown	2 (3.3)	2 (6.7)	0 (0)
Neoadjuvant chemotherapy				0.688
Yes	7 (88.3)	4 (13.3)	3 (10.0)
No	53 (11.7)	26 (86.7)	27 (90.0)

GSRCC: Gastric signet ring cell carcinoma.

Table 3 Fold change of differential genes

Genes	Fold change	P value
Top 10 up-regulated genes
MAGEA2	9182.176	0.000031
MAGEA6	4410.054	0.000429
MAGEA3	2508.358	0.0000307
MAGEA2B	1971.738	0.0000976
ISY1-RAB43	1921.249	0.0000394
MAGEA9	1787.459	0.002399
MAGEA9B	1469.006	0.001587
MAGEA12	1064.08	0.000427
KRT16P6	633.9792	0.043469
NEUROD2	574.5342	0.000245
Top 10 down-regulated genes
REG1B	0.00000891	0.008502
REG1A	0.000149	0.004671
SPINK4	0.000217	0.009491
GIF	0.000237	0.000152
ATOH1	0.000632	0.018238
IGHV4-4	0.000822	0.0000723
GUCA2A	0.000853	0.011982
DMBT1	0.001304	0.001651
SOSTDC1	0.001678	0.000862
ATP4B	0.001709	0.017566