GeneSet Information

Tier III GS14946 • Downregulated gene expression in central nervous system of alcohol-preferring (iP) and non-alcohol preferring (iNP) rats.

DESCRIPTION:

This gene set contains 34 downregulated genes in at least one of five CNS brain regions (nucleus accumbens, amygdale, frontal cortex, caudate putamen, and hippocampus). Background: Study investigates differences in gene expression in five regions of the CNS of inbred alcohol-preferring (iP) and non-alcohol preferring (iNP) rats using microarray gene expression profiling.

LABEL:

DwnReg EtOH iP vs. iNP

SCORE TYPE:

Binary

DATE ADDED:

2009-01-20

DATE UPDATED:

2020-05-06

SPECIES:

AUTHORS:

Kimpel MW, Strother WN, McClintick JN, Carr LG, Liang T, Edenberg HJ, McBride WJ

TITLE:

Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions.

JOURNAL:

Alcohol (Fayetteville, N.Y.) Mar 2007, Vol 41, pp. 95-132

ABSTRACT:

The objective of this study was to determine if there are innate differences in gene expression in selected CNS regions between inbred alcohol-preferring (iP) and -non-preferring (iNP) rats. Gene expression was determined in the nucleus accumbens (ACB), amygdala (AMYG), frontal cortex (FC), caudate-putamen (CPU), and hippocampus (HIPP) of alcohol-naïve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain). Using Linear Modeling for Microarray Analysis with a false discovery rate threshold of 0.1, there were 16 genes with differential expression in the ACB, 54 in the AMYG, 8 in the FC, 24 in the CPU, and 21 in the HIPP. When examining the main effect of strain across regions, 296 genes were differentially expressed. Although the relatively small number of genes found significant within individual regions precluded a powerful analysis for over-represented Gene Ontology categories, the much larger list resulting from the main effect of strain analysis produced 17 over-represented categories (P < .05), including axon guidance, gliogenesis, negative regulation of programmed cell death, regulation of programmed cell death, regulation of synapse structure function, and transmission of nerve impulse. Co-citation analysis and graphing of significant genes revealed a network involved in the neuropeptide Y (NPY) transmitter system. Correlation of all significant genes with those located within previously established rat alcohol QTLs revealed that of the total of 313 significant genes, 71 are located within such QTLs. The many regional and overall gene expression differences between the iP and iNP rat lines may contribute to the divergent alcohol drinking phenotypes of these rats. PUBMED: 17517326
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Annotation Information

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Social Control, Formal (D012926)
Brain (D001921)
Drinking (D004326)
Animals (D000818)
Caudate Nucleus (D002421)
Reproducibility of Results (D015203)
Putamen (D011699)
Principal Component Analysis (D025341)
Gene Regulatory Networks (D053263)
Death (D003643)
Gene Expression Profiling (D020869)
Alcohol Drinking (D000428)
Adult (D000328)
Microarray Analysis (D046228)
Linear Models (D016014)
Rats, Inbred Strains (D011919)
Neuropeptides (D009479)
Neuropeptide Y (D009478)
Overall (D016424)
Reverse Transcriptase Polymerase Chain Reaction (D020133)
Amygdala (D000679)
Rats (D051381)
Nucleus Accumbens (D009714)
Oligonucleotide Array Sequence Analysis (D020411)
Cells (D002477)
Brain Chemistry (D001923)
Nerve Tissue Proteins (D009419)
Cell Death (D016923)
Action Potentials (D000200)
Set (Psychology) (D012718)
Axons (D001369)
Synapses (D013569)
Hippocampus (D006624)
Cluster Analysis (D016000)
amygdala (MA:0000887)
caudate-putamen (MA:0000893)
putamen (MA:0000895)
frontal cortex (MA:0000905)
nerve (MA:0000217)
brain (MA:0000168)
hippocampus (MA:0000191)
cell death (GO:0008219)
negative regulation of programmed cell death (GO:0043069)
gliogenesis (GO:0042063)
cell (GO:0005623)
axon guidance (GO:0007411)
transmission of nerve impulse (GO:0019226)
synapse (GO:0045202)
nucleus (GO:0005634)
programmed cell death (GO:0012501)
regulation of synapse organization (GO:0050807)
regulation of programmed cell death (GO:0043067)
axon (GO:0030424)
death (GO:0016265)
gene expression (GO:0010467)

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Supported by NIH R01 AA18776 jointly funded by NIAAA and NIDA, and JAX Center for Precision Genetics NIH U54 OD 020351