Short-term arginine deprivation results in large-scale modulation of hepatic gene expression in both normal and tumor cells: microarray bioinformatic analysis

Leong, Hwei Xian; Simkevich, Carl; Lesieur-Brooks, Anne; Lau, Bonnie W; Fugere, Celine; Sabo, Edmond; Thompson, Nancy L

doi:10.1186/1743-7075-3-37

Table 3 Arginine sensitivity of rat hepatic cells for known stress response-linked genes.

From: Short-term arginine deprivation results in large-scale modulation of hepatic gene expression in both normal and tumor cells: microarray bioinformatic analysis

A. Normal Hepatic Cells
Annotation	Gene name	Affymetrix ID	Change	P value
Metabolism (Cholesterol biosynthesis)	farensyl diphosphate synthase	1370808_at	↓	0.00002
	farnesyl diphosphate farnesyl transferase 1	1387119_at	↓	0.00011
	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	1373243_at	↓	0.00002
	cytochrome P450, subfamily 51	1368232_at	↓	0.00002
	mevalonate pyrophosphate decarboxylase	1375852_at	↓	0.00043
	7-dehydrocholesterol reductase	1386990_at	↓	0.00013
	mevalonate kinase	1388218_at	↓	0.00002
	isopentenyl-diphosphate delta isomerase	1367839_at	↓	0.00002
	diaphorase 1	1372012_at	↓	0.00077
	Sterol 14 alpha-demethylase (CYP51)	1387020_at	↓	0.00002
	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	1367932_at	↓	0.00002
	phenylalkylamine Ca2+ antagonist (emopamil) binding protein	1367667_at	↓	0.00021
	cytochrome P450, subfamily 51	1368189_at	↓	0.00002
	mevalonate kinase	1368878_at	↓	0.00120
	low density lipoprotein receptor	1388872_at	↓	0.00021
	isopentenyl-diphosphate delta isomerase	1368020_at	↓	0.00002
Metabolism and energy pathways	ATP citrate lyase	1367854_at	↓	0.00002
Metabolism (Urea Cycle)	arginase 1	1368266_at	↓	0.000492
	glutamate dehydrogenase 1	1370200_at	↓	0.00002
	heterogeneous nuclear ribonucleoprotein A/B	1367754_s_at	↓	0.001651
	ornithine aminotransferase	1367729_at	↓	0.002753
	argininosuccinate lyase	1368916_at	↓	0.015426
Growth arrest and DNA damage inducible gene	Gadd45g-predicted	1388792_at	↓	0.00024
	Gadd45b-predicted	1372016_at	↓	0.00778
	Gadd45gip_1predicted	1371896_at	↓	0.00077
Stress Response	growth response protein (CL-6)	1367894_at	↓	0.00002
	voltage-dependent anion channel 1	1386909_a_at	↓	0.00107
Apoptosis	ankyrin-like repeat protein	1367664_at	↓	0.00005
B. Hepatic Tumor Cells
Annotation	Gene name	Affymetrix ID	Change	P value
Metabolism (Cholesterol biosynthesis)	farnesyl diphosphate farnesyl transferase 1	1367839_at	↓	0.00110
	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1	1367932_at	↓	0.00002
	cytochrome P450, subfamily 51	1367979_s_at	↓	0.00014
	7-dehydrocholesterol reductase	1368189_at	↓	0.00043
	isopentenyl-diphosphate delta isomerase	1368878_at	↓	0.00004
	protein kinase, AMP-activated, alpha 1 catalytic subunit	1369104_at	↓	0.05055
	diaphorase 1	1370808_at	↓	0.00304
	Dhcr24-predicted	1372012_at	↓	0.01202
	phenylalkylamine Ca2+ antagonist (emopamil) binding protein	1386990_at	↓	0.00165
	cytochrome P450, subfamily 51	1387020_at	↓	0.00650
	low density lipoprotein receptor	1388218_at	↓	0.00002
	mevalonate pyrophosphate decarboxylase	1368020_at	↑	0.03578
Metabolism and energy pathways	ATP citrate lyase	1367854_at	↓	0.00002
Metabolism (Urea Cycle)	glutamate dehydrogenase 1	1370200_at	↓	0.00359
	glutamate dehydrogenase 1	1387878_at	↓	0.00021
	ornithine aminotransferase	1367729_at	↓	0.00002
	arginase 1	1368266_at	↓	0.00061
Growth arrest & DNA damage inducible gene	Gadd45g-predicted	1388792_at	↓	0.00249
	Gadd45gip_1predicted	1371896_at	↓	0.00133
Stress Response	oxygen regulated protein (150 kD)	1370665_at	↓	0.00141
	solute carrier family 2, (facilitated glucose transporter) member 8	1368286_at	↓	0.00049
	growth response protein (CL-6)	1367894_at	↓	0.00004
	insulin induced gene 2	1389377_at	↑	0.02475
	protease, serine, 25	1367478_at	↑	0.00004
Apoptosis	ankyrin-like repeat protein	1367664_at	↓	0.01202
	glycogen synthase kinase 3 beta	1370267_at	↓	0.00249
	valosin-containing protein	1367455_at	↓	0.03841

Genes were selected based on key word categories/annotations shown and search of Affymetrix rat gene chip probes. Not all genes associated with stress response in human cells are included or identifiable in the rat gene chip. Genes scoring as absent in all 6 normal or tumor samples were eliminated from further analysis. For genes scoring as present, the average value of (+) arginine and (-) arginine was calculated for three replicate samples. Direction of change in expression upon arginine deprivation and the associated p value for such change is presented.

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ISSN: 1743-7075

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