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					GeneSet Title
	Tier III	Human		108 Genes	GS75691 Genes with Altered Expression in Subjects With a History of Alcohol Abuse/Dependence
					LABEL: alcohol history humans DESCRIPTION: from Sokolov et al., 2003
	Tier I	Human	DRG	11 Genes	GS86509 Table 2: Genes with Altered Expression in Subjects With a History of Alcohol Abuse / Dependence Others [DRG]
					LABEL: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DESCRIPTION: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DNA microarray Change in gene expression Eleven subjects with the diagnosis of past (abstinent for a long period -up to 30 years- before death) or current alcohol abuse or dependence, with or without other psychiatric diagnoses (schizophrenia, bipolar disorder, or major depressive disorder) and eleven closely matched control subjects were selected from the Stanley Foundation Brain Bank. Cases were diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Of the cases, five with a history of Affymetrix GeneChip version 4.0 software. Subsequent analyses used Microsoft Excel, Microsoft Access, SPPS 10.5 and S-plus statistical programs. We defined genes with candidate changes in alcohol abuse / dependence as genes for which: 1) the gene showed decreased expression in at least 10 of 11 subjects with alcohol abuse / dependence or showed increased expression in at least 10 of 11 subjects with alcohol abuse / dependence compared to matched nonalcoholics (significance of P < 0.007, Chi-squared = 7.364); 2) the difference in the mean abuser / non-abuser ratio for the gene from a value of 1.0 was significant at P < 0.05 (one sample t-test after natural log transformation of ratios to reduce skewness); 3) hybridization was sufficiently robust that the expression of the gene was called present by Affymetrix criteria in at least one of the samples; and 4) there were no negative mean average difference values in any of the groups (because these represented low-level expression and were therefore of low confidence). (NIF Table ID 195 [121])
	Tier I	Human	DRG	2 Genes	GS86536 Table 2: Genes with Altered Expression in Subjects With a History of Alcohol Abuse / Dependence Unknown function / EST [DRG]
					LABEL: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DESCRIPTION: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DNA microarray Change in gene expression Eleven subjects with the diagnosis of past (abstinent for a long period -up to 30 years- before death) or current alcohol abuse or dependence, with or without other psychiatric diagnoses (schizophrenia, bipolar disorder, or major depressive disorder) and eleven closely matched control subjects were selected from the Stanley Foundation Brain Bank. Cases were diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Of the cases, five with a history of Affymetrix GeneChip version 4.0 software. Subsequent analyses used Microsoft Excel, Microsoft Access, SPPS 10.5 and S-plus statistical programs. We defined genes with candidate changes in alcohol abuse / dependence as genes for which: 1) the gene showed decreased expression in at least 10 of 11 subjects with alcohol abuse / dependence or showed increased expression in at least 10 of 11 subjects with alcohol abuse / dependence compared to matched nonalcoholics (significance of P < 0.007, Chi-squared = 7.364); 2) the difference in the mean abuser / non-abuser ratio for the gene from a value of 1.0 was significant at P < 0.05 (one sample t-test after natural log transformation of ratios to reduce skewness); 3) hybridization was sufficiently robust that the expression of the gene was called present by Affymetrix criteria in at least one of the samples; and 4) there were no negative mean average difference values in any of the groups (because these represented low-level expression and were therefore of low confidence). (NIF Table ID 196 [121])
	Tier I	Human	DRG	15 Genes	GS86896 Table 2: Genes with Altered Expression in Subjects With a History of Alcohol Abuse / Dependence Signal transduction [DRG]
					LABEL: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DESCRIPTION: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DNA microarray Change in gene expression Eleven subjects with the diagnosis of past (abstinent for a long period -up to 30 years- before death) or current alcohol abuse or dependence, with or without other psychiatric diagnoses (schizophrenia, bipolar disorder, or major depressive disorder) and eleven closely matched control subjects were selected from the Stanley Foundation Brain Bank. Cases were diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Of the cases, five with a history of Affymetrix GeneChip version 4.0 software. Subsequent analyses used Microsoft Excel, Microsoft Access, SPPS 10.5 and S-plus statistical programs. We defined genes with candidate changes in alcohol abuse / dependence as genes for which: 1) the gene showed decreased expression in at least 10 of 11 subjects with alcohol abuse / dependence or showed increased expression in at least 10 of 11 subjects with alcohol abuse / dependence compared to matched nonalcoholics (significance of P < 0.007, Chi-squared = 7.364); 2) the difference in the mean abuser / non-abuser ratio for the gene from a value of 1.0 was significant at P < 0.05 (one sample t-test after natural log transformation of ratios to reduce skewness); 3) hybridization was sufficiently robust that the expression of the gene was called present by Affymetrix criteria in at least one of the samples; and 4) there were no negative mean average difference values in any of the groups (because these represented low-level expression and were therefore of low confidence). (NIF Table ID 193 [121])
	Tier I	Human	DRG	5 Genes	GS86996 Table 2: Genes with Altered Expression in Subjects With a History of Alcohol Abuse / Dependence Ubiquitin-proteosome/proteolysis [DRG]
					LABEL: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DESCRIPTION: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DNA microarray Change in gene expression Eleven subjects with the diagnosis of past (abstinent for a long period -up to 30 years- before death) or current alcohol abuse or dependence, with or without other psychiatric diagnoses (schizophrenia, bipolar disorder, or major depressive disorder) and eleven closely matched control subjects were selected from the Stanley Foundation Brain Bank. Cases were diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Of the cases, five with a history of Affymetrix GeneChip version 4.0 software. Subsequent analyses used Microsoft Excel, Microsoft Access, SPPS 10.5 and S-plus statistical programs. We defined genes with candidate changes in alcohol abuse / dependence as genes for which: 1) the gene showed decreased expression in at least 10 of 11 subjects with alcohol abuse / dependence or showed increased expression in at least 10 of 11 subjects with alcohol abuse / dependence compared to matched nonalcoholics (significance of P < 0.007, Chi-squared = 7.364); 2) the difference in the mean abuser / non-abuser ratio for the gene from a value of 1.0 was significant at P < 0.05 (one sample t-test after natural log transformation of ratios to reduce skewness); 3) hybridization was sufficiently robust that the expression of the gene was called present by Affymetrix criteria in at least one of the samples; and 4) there were no negative mean average difference values in any of the groups (because these represented low-level expression and were therefore of low confidence). (NIF Table ID 191 [121])
	Tier I	Human	DRG	21 Genes	GS87031 Table 2: Genes with Altered Expression in Subjects With a History of Alcohol Abuse / Dependence Cell adhesion [DRG]
					LABEL: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DESCRIPTION: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DNA microarray Change in gene expression Eleven subjects with the diagnosis of past (abstinent for a long period -up to 30 years- before death) or current alcohol abuse or dependence, with or without other psychiatric diagnoses (schizophrenia, bipolar disorder, or major depressive disorder) and eleven closely matched control subjects were selected from the Stanley Foundation Brain Bank. Cases were diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Of the cases, five with a history of Affymetrix GeneChip version 4.0 software. Subsequent analyses used Microsoft Excel, Microsoft Access, SPPS 10.5 and S-plus statistical programs. We defined genes with candidate changes in alcohol abuse / dependence as genes for which: 1) the gene showed decreased expression in at least 10 of 11 subjects with alcohol abuse / dependence or showed increased expression in at least 10 of 11 subjects with alcohol abuse / dependence compared to matched nonalcoholics (significance of P < 0.007, Chi-squared = 7.364); 2) the difference in the mean abuser / non-abuser ratio for the gene from a value of 1.0 was significant at P < 0.05 (one sample t-test after natural log transformation of ratios to reduce skewness); 3) hybridization was sufficiently robust that the expression of the gene was called present by Affymetrix criteria in at least one of the samples; and 4) there were no negative mean average difference values in any of the groups (because these represented low-level expression and were therefore of low confidence). (NIF Table ID 192 [121])
	Tier I	Human	DRG	9 Genes	GS87052 Table 2: Genes with Altered Expression in Subjects With a History of Alcohol Abuse / Dependence Transcription / translation / replication [DRG]
					LABEL: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DESCRIPTION: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DNA microarray Change in gene expression Eleven subjects with the diagnosis of past (abstinent for a long period -up to 30 years- before death) or current alcohol abuse or dependence, with or without other psychiatric diagnoses (schizophrenia, bipolar disorder, or major depressive disorder) and eleven closely matched control subjects were selected from the Stanley Foundation Brain Bank. Cases were diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Of the cases, five with a history of Affymetrix GeneChip version 4.0 software. Subsequent analyses used Microsoft Excel, Microsoft Access, SPPS 10.5 and S-plus statistical programs. We defined genes with candidate changes in alcohol abuse / dependence as genes for which: 1) the gene showed decreased expression in at least 10 of 11 subjects with alcohol abuse / dependence or showed increased expression in at least 10 of 11 subjects with alcohol abuse / dependence compared to matched nonalcoholics (significance of P < 0.007, Chi-squared = 7.364); 2) the difference in the mean abuser / non-abuser ratio for the gene from a value of 1.0 was significant at P < 0.05 (one sample t-test after natural log transformation of ratios to reduce skewness); 3) hybridization was sufficiently robust that the expression of the gene was called present by Affymetrix criteria in at least one of the samples; and 4) there were no negative mean average difference values in any of the groups (because these represented low-level expression and were therefore of low confidence). (NIF Table ID 194 [121])
	Tier I	Human	DRG	9 Genes	GS87240 Table 2: Genes with Altered Expression in Subjects With a History of Alcohol Abuse / Dependence Mitochondrial [DRG]
					LABEL: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DESCRIPTION: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DNA microarray Change in gene expression Eleven subjects with the diagnosis of past (abstinent for a long period -up to 30 years- before death) or current alcohol abuse or dependence, with or without other psychiatric diagnoses (schizophrenia, bipolar disorder, or major depressive disorder) and eleven closely matched control subjects were selected from the Stanley Foundation Brain Bank. Cases were diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Of the cases, five with a history of Affymetrix GeneChip version 4.0 software. Subsequent analyses used Microsoft Excel, Microsoft Access, SPPS 10.5 and S-plus statistical programs. We defined genes with candidate changes in alcohol abuse / dependence as genes for which: 1) the gene showed decreased expression in at least 10 of 11 subjects with alcohol abuse / dependence or showed increased expression in at least 10 of 11 subjects with alcohol abuse / dependence compared to matched nonalcoholics (significance of P < 0.007, Chi-squared = 7.364); 2) the difference in the mean abuser / non-abuser ratio for the gene from a value of 1.0 was significant at P < 0.05 (one sample t-test after natural log transformation of ratios to reduce skewness); 3) hybridization was sufficiently robust that the expression of the gene was called present by Affymetrix criteria in at least one of the samples; and 4) there were no negative mean average difference values in any of the groups (because these represented low-level expression and were therefore of low confidence). (NIF Table ID 190 [121])
	Tier I	Human	DRG	108 Genes	GS87261 Table 2: Genes with Altered Expression in Subjects With a History of Alcohol Abuse / Dependence (Whole Table) [DRG]
					LABEL: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DESCRIPTION: Chronic ethanol - Ethanol and abuse / dependence-associated alterations vs. Control DNA microarray Change in gene expression Eleven subjects with the diagnosis of past (abstinent for a long period -up to 30 years- before death) or current alcohol abuse or dependence, with or without other psychiatric diagnoses (schizophrenia, bipolar disorder, or major depressive disorder) and eleven closely matched control subjects were selected from the Stanley Foundation Brain Bank. Cases were diagnosed according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Of the cases, five with a history of Affymetrix GeneChip version 4.0 software. Subsequent analyses used Microsoft Excel, Microsoft Access, SPPS 10.5 and S-plus statistical programs. We defined genes with candidate changes in alcohol abuse / dependence as genes for which: 1) the gene showed decreased expression in at least 10 of 11 subjects with alcohol abuse / dependence or showed increased expression in at least 10 of 11 subjects with alcohol abuse / dependence compared to matched nonalcoholics (significance of P < 0.007, Chi-squared = 7.364); 2) the difference in the mean abuser / non-abuser ratio for the gene from a value of 1.0 was significant at P < 0.05 (one sample t-test after natural log transformation of ratios to reduce skewness); 3) hybridization was sufficiently robust that the expression of the gene was called present by Affymetrix criteria in at least one of the samples; and 4) there were no negative mean average difference values in any of the groups (because these represented low-level expression and were therefore of low confidence). (NIF Method ID 121)

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