List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Fasting plasma glucose. The EFO term fasting blood glucose measurement was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.
Cerebellum differential expression analysis of genotype by time effects in Pax6 mice and controls. This set contains genes for which there is an additive effect of the mutation and linear increase in both mutant and wild types through time.
Activation of the mesolimbic dopamine reward pathway by acute ethanol produces reinforcement and changes in gene expression that appear to be crucial to the molecular basis for adaptive behaviors and addiction. The inbred mouse strains DBA/2J and C57BL/6J exhibit contrasting acute behavioral responses to ethanol. We used oligonucleotide microarrays and bioinformatics methods to characterize patterns of gene expression in three brain regions of the mesolimbic reward pathway of these strains. Expression profiling included examination of both differences in gene expression 4 h after saline injection or acute ethanol (2 g/kg). Using a rigorous stepwise method for microarray analysis, we identified 788 genes differentially expressed in control DBA/2J versus C57BL/6J mice and 307 ethanol-regulated genes in the nucleus accumbens, prefrontal cortex, and ventral tegmental area. There were strikingly divergent patterns of ethanol-responsive gene expression in the two strains. Ethanol-responsive genes also showed clustering at discrete chromosomal regions, suggesting local chromatin effects in regulation. Ethanol-regulated genes were generally related to neuroplasticity, but regulation of discrete functional groups and pathways was brain region specific: glucocorticoid signaling, neurogenesis, and myelination in the prefrontal cortex; neuropeptide signaling and developmental genes, including factor Bdnf, in the nucleus accumbens; and retinoic acid signaling in the ventral tegmental area. Bioinformatics analysis identified several potential candidate genes for quantitative trait loci linked to ethanol behaviors, further supporting a role for expression profiling in identifying genes for complex traits. Brain region-specific changes in signaling and neuronal plasticity may be critical components in development of lasting ethanol behavioral phenotypes such as dependence, sensitization, and craving.
Affymetrix oligonucleotide arrays to assess gene expression in brains of mice selectively bred for differences in acute functional tolerance to an incoordinating effect of ethanol (HAFT mice, high acute functional tolerance; LAFT mice, low acute functional tolerance)
Sixty candidate genes upregulated in mouse midbrain 2 h post-ethanol treatment identified by microarray analysis were filtered by WebQTL analysis to derive the 49 genes shown
Two strains of inbred mice, C57BL/6J and DBA/2J, were exposed to acute dose of ethanol and following microarray expression profiles in these two strains, study identified genes that are differentially expressed during ethanol treatment. This gene set comprises 30 ethanol-dependent genes that were upregulated in C57BL/6j mice during the study.
This gene set comprises 30 ethanol-dependent genes that were upregulated in DBA/2J mice during the study. Background: Two strains of inbred mice, C57BL/6J and DBA/2J, were exposed to acute dose of ethanol and following microarray expression profiles in these two strains, study identified genes that are differentially expressed during ethanol treatment.
A list of the 307 genes found to be upregulated or downregulated by ethanol in PFC, VTA or NA of B6 or D2 mice. ID number represents cluster membership from Figure 4.
Authors:
Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Sikela JM, Williams RW, Miles MF
A list of genes whose transcript abundance in the PFC changed significantly 4 hours after an acute dose of ethanol (1.8 g/kg). This list was generated using Fisher's Combined Probability test to analyze saline vs ethanol S-scores across B6 and D2 inbred strains (n=3) and 27 BXD RI lines (n=1). Statistical significance was determined using 1,000 permutations of S-score data and selecting for probe-sets with q-values < 0.05. Aaron Wolen 5-26-10.
Authors:
Wolen AR, Phillips CA, Langston MA, Putman AH, Vorster PJ, Bruce NA, York TP, Williams RW, Miles MF
QTL for METH responses for body temperature on Chr8 at D8Ncvs43 (95.66 Mbp , Build 37)
Description:
METH responses for body temperature spans 70.66 - 120.66 Mbp (NCBI Build 37) on Chr8. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Ethanol induced LORR Chr# 8 rs3666140 (44049661) with right flanking marker rs3661760(24557766) and left marker rs13479995 (116236688). This was mapped in 300 + (b6x129)F2 mice.
Ethanol Induced Ataxia Chr#8 rs3699406 (72486070) with right flanking marker rs6386110 (45897379) and left marker rs13479995(116236688). This was mapped in 300 + (b6x129)F2 mice.
GeneWeaver