Claudin 1 mediates tumor necrosis factor alpha-induced cell migration in human gastric cancer cells

Table 1 Genes that displayed the greatest changes in their expressions in the claudin 1 small interfering RNA transfected MKN28 cells

Gene symbol	Gene ID	Gene name	Fold change
Up-regulated genes
FGF6	NM_020996	Fibroblast growth factor 6	151.34
TM4SF20	NM_024795	Transmembrane 4 L six family member 20	72.03
B4GALNT2	NM_153446	Beta-1,4-N-acetyl-galactosaminyl transferase 2	47.30
SLC2A13	BC047507	Solute carrier family 2 (facilitated glucose transporter), member 13	43.02
HS3ST2	NM_006043	Heparan sulfate (glucosamine) 3-O-sulfotransferase 2	28.39
ZNF596	NM_001042416	Zinc finger protein 596	26.36
IL2RA	NM_000417	Interleukin 2 receptor, alpha	22.00
CCL2	NM_002982	Chemokine (C-C motif) ligand 2	18.05
SGOL2	BC048349	Shugoshin-like 2	17.64
SYT4	NM_020783	Synaptotagmin IV	17.29
FGF19	NM_005117	Fibroblast growth factor 19	16.44
ARID5B	NM_032199	AT rich interactive domain 5B	14.47
DEFB105B	NM_001040703	Defensin, beta 105B	14.34
DSG3	NM_001944	Desmoglein 3	12.99
RSPH1	NM_080860	Radial spoke head 1 homolog (Chlamydomonas)	12.82
COL5A2	NM_000393	Collagen, type V, alpha 2	12.72
NRG2	NM_013982	Neuregulin 2	12.63
TMEM26	NM_178505	Transmembrane protein 26	12.22
CCL3L3	NM_001001437	Chemokine (C-C motif) ligand 3-like 3	11.54
OR51E1	NM_152430	Olfactory receptor, family 51, subfamily E, member 1	9.43
Down-regulated genes
LY6G6F	NM_001003693	Lymphocyte antigen 6 complex, locus G6F	-332.04
WT1	NM_024426	Wilms tumor 1	-68.28
MADCAM1	NM_130760	Mucosal vascular addressin cell adhesion molecule 1	-60.84
SLC2A9	NM_001001290	Solute carrier family 2 (facilitated glucose transporter), member 9	-48.05
SULT4A1	NM_014351	Sulfotransferase family 4A, member 1	-39.30
SYNPR	NM_144642	Synaptoporin	-36.73
C10orf47	NM_153256	Chromosome 10 open reading frame 47	-29.96
MAS1L	NM_052967	MAS1 oncogene-like	-29.67
CLDN1	NM_021101	Claudin 1	-26.87
CBX1	NM_006807	Chromobox homolog 1	-26.37
MPPED2	NM_001145399	Metallophosphoesterase domain containing 2	-25.00
SCUBE2	NM_020974	Signal peptide, CUB domain, EGF-like 2	-22.13
CHI3L2	NM_001025199	Chitinase 3-like 2	-21.67
SLIT2	NM_004787	Slit homolog 2	-21.60
HFM1	NM_001017975	HFM1, ATP-dependent DNA helicase homolog	-20.56
CR1	NM_000651	Complement component (3b/4b) receptor 1	-18.04
PLA2G10	NM_003561	Phospholipase A2, group X	-16.70
GRIP2	NM_001080423	Glutamate receptor interacting protein 2	-16.45
XIST	NR_001564	X (inactive)-specific transcript	-15.79
TNF-SF10	NM_003810	Tumor necrosis factor (ligand) superfamily, member 10	-15.26

Table 2 Top molecular and cellular functions, upstream regulators, and networks of claudin1 according to ingenuity pathway analysis

Name	P value	Molecules	Score
Top molecular and cellular functions
Cellular movement	2.77 × 10-9-1.01 × 10-2	51
Cell-to-cell signaling and interaction	7.24 × 10-7-1.02 × 10-2	55
Molecular transport	1.23 × 10-6-9.98 × 10-3	51
Small molecule biochemistry	1.23 × 10-6-9.98 × 10-3	55
Cellular development	3.80 × 10-6-9.50 × 10-3	59
Top upstream regulators
TNF-RSF1A	1.80 × 10-7
TNF-	1.70 × 10-6
NF-κB (complex)	2.01 × 10-6
Escherichia coli B5 lipopolysaccharide	2.09 × 10-6
NF-κB1	3.23 × 10-6
Top networks
Associated network functions
Cellular assembly and organization, hair and skin development and function, cellular function and maintenance			33
Cell-to-cell signaling and interaction, cellular growth and proliferation, tissue morphology			32
Cellular movement, hematological system development and function, immune cell trafficking			31
Cardiovascular system development and function, organismal development, cellular movement			22
Hereditary disorder, respiratory disease, tissue development			22

TNF-: Tumor necrosis factor; NF: Nuclear factor.

Table 3 Top 10 up or down-regulated genes induced by tumor necrosis factor α in control small interfering RNA or claudin 1 small interfering RNA transfected MKN28 cells

Gene symbol	Gene ID	Gene name	Control siRNA	Claudin1 siRNA
			Fold change	Fold change
Up-regulated genes
IL6	NM_000600	Interleukin 6	11.16	7.16
MMP9	NM_004994	Matrix metallopeptidase 9	10.49	18.13
BMP2	NM_001200	Bone morphogenetic protein 2	10.12	5.62
VSTM1	NM_198481	V-set and transmembrane domain containing 1	9.83	2.53
CLEC1A	NM_016511	C-type lectin domain family 1, member A	9.71	-1.22
CXCL10	NM_001565	Chemokine (C-X-C motif) ligand 10	9.33	1.82
IL2RG	NM_000206	Interleukin 2 receptor, gamma	9.14	15.56
TFPI	NM_001032281	Tissue factor pathway inhibitor	8.98	11.79
KLHDC7B	NM_138433	Kelch domain containing 7B	8.90	1.79
CCL5	NM_002985	Chemokine (C-C motif) ligand 5	8.85	7.84
Down-regulated genes
LY6G6F	NM_001003693	Lymphocyte antigen 6 complex, locus G6F	-311.81	1.05
RFTN2	NM_144629	Raftlin family member 2	-291.41	1.39
WT1	NM_024426	Wilms tumor 1	-75.96	1.05
MADCAM1	NM_130760	Mucosal vascular addressin cell adhesion molecule 1	-67.39	1.06
SLC2A9	NM_001001290	Solute carrier family 2, member 9	-49.12	-1.21
C10orf47	NM_153256	Chromosome 10 open reading frame 47	-44.11	1.85
SYNPR	NM_144642	Synaptoporin	-40.64	1.08
GGT7	NM_178026	Gamma-glutamyltransferase 7	-40.33	1.24
LRRC36	NM_018296	Leucine rich repeat containing 36	-38.25	1.06
MAS1L	NM_052967	MAS1 oncogene-like	-32.62	1.07