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 Alzheimer's disease (late onset). The EFO term Alzheimers disease 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:
X Hu, E Pickering, YC Liu, S Hall, H Fournier, E Katz, B Dechairo, S John, P Van Eerdewegh, H Soares
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 Alzheimer's disease. The EFO term Alzheimers disease 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:
MI Kamboh, FY Demirci, X Wang, RL Minster, MM Carrasquillo, VS Pankratz, SG Younkin, AJ Saykin, G Jun, C Baldwin, MW Logue, J Buros, L Farrer, MA Pericak-Vance, JL Haines, RA Sweet, M Ganguli, E Feingold, ST Dekosky, OL Lopez, MM Barmada
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 Alzheimer's disease (late onset). The EFO term Alzheimers disease 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:
EM Wijsman, ND Pankratz, Y Choi, JH Rothstein, KM Faber, R Cheng, JH Lee, TD Bird, DA Bennett, R Diaz-Arrastia, AM Goate, M Farlow, B Ghetti, RA Sweet, TM Foroud, R Mayeux
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 Alzheimer's disease (late onset). The EFO term Alzheimers disease 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:
AC Naj, G Jun, GW Beecham, LS Wang, BN Vardarajan, J Buros, PJ Gallins, JD Buxbaum, GP Jarvik, PK Crane, EB Larson, TD Bird, BF Boeve, NR Graff-Radford, PL De Jager, D Evans, JA Schneider, MM Carrasquillo, N Ertekin-Taner, SG Younkin, C Cruchaga, JS Kauwe, P Nowotny, P Kramer, J Hardy, MJ Huentelman, AJ Myers, MM Barmada, FY Demirci, CT Baldwin, RC Green, E Rogaeva, P St George-Hyslop, SE Arnold, R Barber, T Beach, EH Bigio, JD Bowen, A Boxer, JR Burke, NJ Cairns, CS Carlson, RM Carney, SL Carroll, HC Chui, DG Clark, J Corneveaux, CW Cotman, JL Cummings, C DeCarli, ST DeKosky, R Diaz-Arrastia, M Dick, DW Dickson, WG Ellis, KM Faber, KB Fallon, MR Farlow, S Ferris, MP Frosch, DR Galasko, M Ganguli, M Gearing, DH Geschwind, B Ghetti, JR Gilbert, S Gilman, B Giordani, JD Glass, JH Growdon, RL Hamilton, LE Harrell, E Head, LS Honig, CM Hulette, BT Hyman, GA Jicha, LW Jin, N Johnson, J Karlawish, A Karydas, JA Kaye, R Kim, EH Koo, NW Kowall, JJ Lah, AI Levey, AP Lieberman, OL Lopez, WJ Mack, DC Marson, F Martiniuk, DC Mash, E Masliah, WC McCormick, SM McCurry, AN McDavid, AC McKee, M Mesulam, BL Miller, CA Miller, JW Miller, JE Parisi, DP Perl, E Peskind, RC Petersen, WW Poon, JF Quinn, RA Rajbhandary, M Raskind, B Reisberg, JM Ringman, ED Roberson, RN Rosenberg, M Sano, LS Schneider, W Seeley, ML Shelanski, MA Slifer, CD Smith, JA Sonnen, S Spina, RA Stern, RE Tanzi, JQ Trojanowski, JC Troncoso, VM Van Deerlin, HV Vinters, JP Vonsattel, S Weintraub, KA Welsh-Bohmer, J Williamson, RL Woltjer, LB Cantwell, BA Dombroski, D Beekly, KL Lunetta, ER Martin, MI Kamboh, AJ Saykin, EM Reiman, DA Bennett, JC Morris, TJ Montine, AM Goate, D Blacker, DW Tsuang, H Hakonarson, WA Kukull, TM Foroud, JL Haines, R Mayeux, MA Pericak-Vance, LA Farrer, GD Schellenberg
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 Systemic lupus erythematosus. The EFO term systemic lupus erythematosus 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:
DL Armstrong, R Zidovetzki, ME Alarcón-Riquelme, BP Tsao, LA Criswell, RP Kimberly, JB Harley, KL Sivils, TJ Vyse, PM Gaffney, CD Langefeld, CO Jacob
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 Neurofibrillary tangles. The EFO term neurofibrilliary tangles 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.
Authors:
GW Beecham, K Hamilton, AC Naj, ER Martin, M Huentelman, AJ Myers, JJ Corneveaux, J Hardy, JP Vonsattel, SG Younkin, DA Bennett, PL De Jager, EB Larson, PK Crane, MI Kamboh, JK Kofler, DC Mash, L Duque, JR Gilbert, H Gwirtsman, JD Buxbaum, P Kramer, DW Dickson, LA Farrer, MP Frosch, B Ghetti, JL Haines, BT Hyman, WA Kukull, RP Mayeux, MA Pericak-Vance, JA Schneider, JQ Trojanowski, EM Reiman, GD Schellenberg, TJ Montine
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 Dementia and core Alzheimer's disease neuropathologic changes. The EFO term dementia, Alzheimer's disease neuropathologic change 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:
GW Beecham, K Hamilton, AC Naj, ER Martin, M Huentelman, AJ Myers, JJ Corneveaux, J Hardy, JP Vonsattel, SG Younkin, DA Bennett, PL De Jager, EB Larson, PK Crane, MI Kamboh, JK Kofler, DC Mash, L Duque, JR Gilbert, H Gwirtsman, JD Buxbaum, P Kramer, DW Dickson, LA Farrer, MP Frosch, B Ghetti, JL Haines, BT Hyman, WA Kukull, RP Mayeux, MA Pericak-Vance, JA Schneider, JQ Trojanowski, EM Reiman, GD Schellenberg, TJ Montine
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.
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
Whole Brain Gene Expression Correlates for BEC measured in BXD RI Females & Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The BEC measures blood ethanol concentration in mg/dl 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
Neocortex Gene Expression Correlates for MDMA_ACT_MDA_1 measured in BXD RI Females & Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The MDMA_ACT_MDA_1 measures Locomotor response of 10 mg/kg MDMA injected on Day 2 under the domain MDMA. 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
Neocortex Gene Expression Correlates for MDMA_ACT_MDA_1 measured in BXD RI Females obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The MDMA_ACT_MDA_1 measures Locomotor response of 10 mg/kg MDMA injected on Day 2 under the domain MDMA. 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
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
Acute nicotine - Nicotine vs. Saline DNA microarray Change in gene expression All the animals received a subcutaneous saline injection once daily for 5 days to habituate them to the injection process. On day 6, animals received a subcutaneous injection of saline or nicotine in saline (2 mg / kg). Animals were killed by cervical dislocation 1, 2, 4, or 6 h following saline or nicotine injection. S-score (significance score) algorithm Change in expression at 6 hours. S-scores (significance score) > / = 2 or < / = -2 consistently in two adjacent time-points from the 1-, 2-, 4- and 6-h time-points. For a comparison between two arrays, an S-score of 2 or ?2 corresponds to a P value of 0.046. (NIF Table ID 339 [192])
Authors:
Chen X, Che Y, Zhang L, Putman AH, Damaj I, Martin BR, Kendler KS, Miles MF
Genes associated with Homo sapiens that interact with the MeSH term 'Smoke' (D012906). Incorporates data from 54 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 'Paraquat' (D010269). Incorporates data from 793 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 'Vitamin E' (D014810). 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 'nickel sulfate' (C029938). 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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