NF-kB and ERK-signaling pathways contribute to the gene expression induced by cag PAI-positive-Helicobacter pylori infection

Table 1 Primer sequences for RT-PCR

Genes	Forward	Reverse
IL-8	5’-GCT TTC TGA TGG AAG AGA GC-3’	5’-GGC ACA GTG GAA CAA GGA CT-3’
c-fos	5’-GTC AAG AGC ATC AGC AGCA T-3’	5’-TCG GGG TAG GTG AAG ACG AA-3’
HNRPDL	5’-GTT TCA GAG GAC CTG GAA TA-3’	5’-TCA CTA CCC TAG ACA CCG CA3’
Vinculin	5’-CAA GTG TGA CCG AGT GGA CC-3’	5’-TTG GTA TCA ATG GCT TCG TC-3’
DSS1	5’-CAA GTC TCT ATG GTA GCG TCA GC-3’	5’-ACC ATG TTT CTC TAG TTC AG-3’
NDRG1	5’-GGC GCG ACC TGG AGA TGAG-3’	5’-CTA GCA GGA GAC CTC CAT GG-3’
EMK-1	5’-GAG ATG GAG GTG TGC AAA CT-3’	5’-TGG TTT AGG CGA AAT ACT CT-3’
GAPDH	5’-ACC ACA GTC CAT GCC ATC AC-3’	5’-TCC ACC ACC CTG TTG CTG TA-3’

Table 2 The functional profiles of the H pylori-induced changes in gene expression in vitro. Cluster represents the assigned cluster numbers in Figure 1C. Functions were defined by using the Onto-Express program, using hypergeometric distribution to determine the significance of differences (n≥5, P<0.05, see Materials and methods)

Cluster	Function	No. of the genes (Total)	P-value
C-1	Chaperon activity	12 (31)	0.019
	Transcription regulator activity	29 (92)	0.033
C-2	Apoptosis regulator activity	7 (9)	<0.01
	Cell adhesion molecule activity	18 (39)	<0.01
	Signal transducer activity	47 (132)	0.034
	Transcription regulator activity	9 (20)	0.037
	Structural molecular activity	40 (113)	0.049
C-3	Antioxidant activity	6 (8)	<0.01
C-4	Lyase activity	8 (10)	0.011
	Chaperon activity	10 (31)	0.037

Table 3 Genes undergoing most striking upregulation during H pylori-infection in vitro. Values show the mean change in gene expression from two separate microarray experiments in vitro(shown at “1.5, 3, 6, and 12 h”. Significantly upregulated values are shown in bold (above threefold)

Acc. Number	Gene Symbol	Name	Function	1.5h	3h	6h	12h
U79243	LZTR1	leucine-zipper-like transcriptional regulator 1	transcription	5.08	3.08	0.95	2.30
X61118	LMO2	LIM domain only 2 (rhombotin-like 1)	tumor associated	2.53	16.24	0.28	1.04
BC004247	RAC1	ras-related C3 botulinum toxin substrate 1 (rho family small GTP binding protein Rac1)	adhesion/cytoskeleton	1.13	4.78	0.89	1.29
AF005043	PARG	poly (ADP-ribose) glycohydrolase	metabolism	0.58	0.62	14.72	0.53
U86782	POH1	26S proteasome-associated pad1 homolog	RNA/Protein processing	2.55	3.59	7.24	3.56
M62839	APOH	apolipoprotein H (beta-2-glycoprotein I)	immunity	0.49	3.49	0.65	1.47
BC004980	SLC25A1	solute carrier family 25 (mitochondrial carrier; citrate transporter) member 1	metabolism	4.07	0.81	0.95	1.54
Z26649	PLCB3	phospholipase C beta 3 (phosphatidylinositol-specific)	tumor associated	2.49	3.32	0.75	2.52
M62399	RELA	v-rel reticuloendotheliosis viral oncogene homolog A nuclear factor of kappa light polypeptide gene enhancer in B-cells 3 p65 (avian)	apoptpsis	2.84	3.24	1.43	1.13
BC000665	TCP1	t-complex 1	RNA/Protein processing	1.73	3.21	1.05	1.41
V01512	c-fos	V01512|HSCFOS Human cellular oncogene c-fos (complete sequence).	tumor associated	37.81	2.48	0.57	0.91
BC000117	GMDS	GDP-mannose 46-dehydratase	metabolism	2.63	4.37	2.28	3.75
L29218	CLK2	CDC-like kinase 2	growth/maintenance	1.46	4.03	1.96	0.60
BC000771	NTRK1	neurotrophic tyrosine kinase receptor type 1	tumor associated	3.33	3.47	1.42	3.59
X68836	MAT2A	methionine adenosyltransferase II alpha	metabolism	3.14	2.95	0.85	1.28
X94232	MAPRE2	microtubule-associated protein RP/EB family member 2	growth/maintenance	0.58	3.23	0.69	0.29
X80200	TRAF4	TNF receptor-associated factor 4	signal transduction	3.20	3.02	3.67	1.08
D76444	ZFP103	zinc finger protein 103 homolog (mouse)	growth/maintenance	1.38	2.63	3.99	1.78