Publication Details

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

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

4 GeneSets from this Publication:


Select gene sets below using the check boxes, and then add them to a project using the pull down below. You can also create a project using the pull down. To view a set, click on the GeneSetID:GeneSet Description shown in green below.
Expand Tier III Rat 41 Genes GS14945: Upregulated gene expression in CNS of alcohol-preferring (iP) and non-alcohol preferring (iNP) rats.
Expand Tier III Rat 20 Genes GS14946: Downregulated gene expression in CNS of alcohol-preferring (iP) and non-alcohol preferring (iNP) rats.
Expand Tier III Rat 43 Genes GS14947: Differential expression of ethanol non-alcohol preferring (iNP) rats vs. inbred alcohol-preferring (iP) rats with greater expression iNP rats than in iP rats
Expand Tier III Rat 30 Genes GS14948: Differential expression of ethanol non-alcohol preferring (iNP) rats vs. inbred alcohol-preferring (iP) rats with greater expression iP rats than in iNP rats