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 Amyotrophic lateral sclerosis (sporadic). The EFO term sporadic amyotrophic lateral sclerosis 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.
Authors:
T Xie, L Deng, P Mei, Y Zhou, B Wang, J Zhang, J Lin, Y Wei, X Zhang, R Xu
Preference for 10% ethanol (g/kg) in tap water offered vs. tap water; means are the average of days 2 and 4 of a 4-day 24-hr access period by Phillips TJ , et al
Whole Brain Gene Expression Correlates for LM_CUE_ACTIVITY measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The LM_CUE_ACTIVITY measures Activity in altered context during presentation of cue under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Whole Brain Gene Expression Correlates for LM_CUE_SUPPRESS measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The LM_CUE_SUPPRESS measures Suppression of activity in altered context under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Hippocampus Gene Expression Correlates for ROTATRAIN_DIFF measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The ROTATRAIN_DIFF measures Difference in time on rotarod between training and saline under the domain Ethanol. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Cerebellum Gene Expression Correlates for ADRE_LEFT_WT measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The ADRE_LEFT_WT measures Left adrenal weight under the domain Adrenals. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Cerebellum Gene Expression Correlates for ADRE_RIGHT_WT measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The ADRE_RIGHT_WT measures Right adrenal weight under the domain Adrenals. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Whole Brain Gene Expression Correlates for HIC_SCORE measured in BXD RI Females & Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The HIC_SCORE measures Handling induced convulsion score under the domain Ethanol HIC. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
cocaine related behavior 4 (Cocrb4) spans 120.266777 - 170.266777 Mbp (NCBI Build 37) on Chr 3. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
QTL for cocaine related behavior on Chr3 at D3Ncvs49 (145.27 Mbp , Build 37)
Description:
cocaine related behavior spans 120.27 - 170.27 Mbp (NCBI Build 37) on Chr3. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL spans- 118.3-168.3 Mbp (NCBI Build 37) on Chr3. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org). Ethanol consumption in mice was analyzed in selectively breed mice derived from an F2 population of intercrossed (C57BL/6J x DBA/2J)F1 mice. Whereas C57BL/6J are high consumers of alcohol and DBA/2J are low consumers. The concentration of ethanol used was 10%. With low preference mice and high preference mice mated for a maximum of 4 generations. In generation 4 of the Low selected line a significant QTL was observed and associated with D3Mit17. Authors suggest Adh1 may be a candidate gene.
QTL for METH responses for body temperature on Chr3 at P40-rs4 (154.89 Mbp , Build 37)
Description:
METH responses for body temperature spans 129.89 - 179.89 Mbp (NCBI Build 37) on Chr3. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
None - Basal gene expression profiles between C57BL/6J, DBA/2J, 129P3/J, and SWR/J strains DNA microarray Change in gene expression Two-way analysis of variance (ANOVA). 3,457 probe sets (corresponded to 2,870 different transcripts) with significant inter-strain differences (differ by at least 1.2-fold) - False discovery rate [FDR] < 1%, , rank > 3. Such a large disparity in the mouse striatal transcriptome was estimated by comparing nine array replicates prepared per strain from all of the treatment groups. More than half of the identified probe sets exhibited markedly significant results (1,735 with rank > 7). (NIF Method ID 84.1)
Authors:
Korostynski M, Piechota M, Kaminska D, Solecki W, Przewlocki R
Genes associated with Homo sapiens that interact with the MeSH term 'entinostat' (C118739). Incorporates data from 11 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Arsenic' (D001151). Incorporates data from 87 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term '5,5'-bis(8-(phenylamino)-1-naphthalenesulfonate)' (C035763). Incorporates data from 1 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Dihydrotestosterone' (D013196). Incorporates data from 6 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term '(6-(4-(2-piperidin-1-ylethoxy)phenyl))-3-pyridin-4-ylpyrazolo(1,5-a)pyrimidine' (C516138). Incorporates data from 3 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'resveratrol' (C059514). Incorporates data from 16 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Arbutin' (D001104). Incorporates data from 68 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Gambusia holbrooki that interact with the MeSH term 'Endocrine Disruptors' (D052244). Incorporates data from 1 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
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