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 Adiposity. The EFO term obesity 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:
TO Kilpeläinen, MC Zillikens, A Stančákova, FM Finucane, JS Ried, C Langenberg, W Zhang, JS Beckmann, J Luan, L Vandenput, U Styrkarsdottir, Y Zhou, AV Smith, JH Zhao, N Amin, S Vedantam, SY Shin, T Haritunians, M Fu, MF Feitosa, M Kumari, BV Halldorsson, E Tikkanen, M Mangino, C Hayward, C Song, AM Arnold, YS Aulchenko, BA Oostra, H Campbell, LA Cupples, KE Davis, A Döring, G Eiriksdottir, K Estrada, JM Fernández-Real, M Garcia, C Gieger, NL Glazer, C Guiducci, A Hofman, SE Humphries, B Isomaa, LC Jacobs, A Jula, D Karasik, MK Karlsson, KT Khaw, LJ Kim, M Kivimäki, N Klopp, B Kühnel, J Kuusisto, Y Liu, O Ljunggren, M Lorentzon, RN Luben, B McKnight, D Mellström, BD Mitchell, V Mooser, JM Moreno, S Männistö, JR O'Connell, L Pascoe, L Peltonen, B Peral, M Perola, BM Psaty, V Salomaa, DB Savage, RK Semple, T Skaric-Juric, G Sigurdsson, KS Song, TD Spector, AC Syvänen, PJ Talmud, G Thorleifsson, U Thorsteinsdottir, AG Uitterlinden, CM van Duijn, A Vidal-Puig, SH Wild, AF Wright, DJ Clegg, E Schadt, JF Wilson, I Rudan, S Ripatti, IB Borecki, AR Shuldiner, E Ingelsson, JO Jansson, RC Kaplan, V Gudnason, TB Harris, L Groop, DP Kiel, F Rivadeneira, M Walker, I Barroso, P Vollenweider, G Waeber, JC Chambers, JS Kooner, N Soranzo, JN Hirschhorn, K Stefansson, HE Wichmann, C Ohlsson, S O'Rahilly, NJ Wareham, EK Speliotes, CS Fox, M Laakso, RJ Loos
GWAS: type II diabetes mellitus, autoantibody measurement
Description:
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 Type 2 diabetes and other traits. The EFO term type II diabetes mellitus, autoantibody 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:
J Rung, S Cauchi, A Albrechtsen, L Shen, G Rocheleau, C Cavalcanti-Proença, F Bacot, B Balkau, A Belisle, K Borch-Johnsen, G Charpentier, C Dina, E Durand, P Elliott, S Hadjadj, MR Järvelin, J Laitinen, T Lauritzen, M Marre, A Mazur, D Meyre, A Montpetit, C Pisinger, B Posner, P Poulsen, A Pouta, M Prentki, R Ribel-Madsen, A Ruokonen, A Sandbaek, D Serre, J Tichet, M Vaxillaire, JF Wojtaszewski, A Vaag, T Hansen, C Polychronakos, O Pedersen, P Froguel, R Sladek
GWAS: insulin sensitivity measurement, body mass index
Description:
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 Modified Stumvoll Insulin Sensitivity Index (interaction with BMI). The EFO term insulin sensitivity measurement, body mass index 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:
GA Walford, S Gustafsson, D Rybin, A Stančáková, H Chen, CT Liu, J Hong, RA Jensen, K Rice, AP Morris, R Mägi, A Tönjes, I Prokopenko, ME Kleber, G Delgado, G Silbernagel, AU Jackson, EV Appel, N Grarup, JP Lewis, ME Montasser, C Landenvall, H Staiger, J Luan, TM Frayling, MN Weedon, W Xie, S Morcillo, MT Martínez-Larrad, ML Biggs, YD Chen, A Corbaton-Anchuelo, K Færch, JM Gómez-Zumaquero, MO Goodarzi, JR Kizer, HA Koistinen, A Leong, L Lind, C Lindgren, F Machicao, AK Manning, GM Martín-Núñez, G Rojo-Martínez, JI Rotter, DS Siscovick, JM Zmuda, Z Zhang, M Serrano-Rios, U Smith, F Soriguer, T Hansen, TJ Jørgensen, A Linnenberg, O Pedersen, M Walker, C Langenberg, RA Scott, NJ Wareham, A Fritsche, HU Häring, N Stefan, L Groop, JR O'Connell, M Boehnke, RN Bergman, FS Collins, KL Mohlke, J Tuomilehto, W März, P Kovacs, M Stumvoll, BM Psaty, J Kuusisto, M Laakso, JB Meigs, J Dupuis, E Ingelsson, JC Florez
This gene set comprises 399 genes that are differentially expressed within each of five brain regions (amygdale, hippocampus, nucleus accumbens, prefrontal cortex and ventral tegmental area) when chronic nicotine treatment is administered to C3H/HeJ mice only. Background: Studies involving use of chronic nicotine treatment identify unique nicotine addiction genes and the biological processes they control in B6 and C3 mice. Results are obtained using gene expression profiling and gene ontology.
Authors:
Wang J, Gutala R, Hwang YY, Kim JM, Konu O, Ma JZ, Li MD
Striatum Gene Expression Correlates for ROTAETHA_TIME measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The ROTAETHA_TIME measures Mean time on rotarod following ethanol 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
Striatum Gene Expression Correlates for SHAKE measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The SHAKE measures Morphine - wet dog shakes under the domain Morphine. 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
Striatum Gene Expression Correlates for SHAKE measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The SHAKE measures Morphine - wet dog shakes under the domain Morphine. 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 1 (Cocrb1) spans 79.870166 - 121.405905 Mbp (NCBI Build 37) on Chr 1. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
QTL for METH responses for body temperature on Chr1 at D1Ncvs75 (79.87 Mbp , Build 37)
Description:
METH responses for body temperature spans 54.87 - 104.87 Mbp (NCBI Build 37) on Chr1. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for chronic alcohol withdrawal severity on Chr1 at D1Mit46 (83.89 Mbp , Build 37)
Description:
chronic alcohol withdrawal severity spans 58.89 - 108.89 Mbp (NCBI Build 37) on Chr1. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Authors:
Bergeson SE, Kyle Warren R, Crabbe JC, Metten P, Gene Erwin V, Belknap JK
QTL for METH responses for home cage activity on Chr1 at D1Ncvs41 (101.77 Mbp , Build 37)
Description:
METH responses for home cage activity spans 76.77 - 126.77 Mbp (NCBI Build 37) on Chr1. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Chronic cocaine - Cocaine-paired (conditioned place preference) vs. Control (saline or cocaine-non-paired) DNA microarray All genes on microarray presented After the pre-conditioning phase where animals were allowed access to either compartment for 15 minutes for 4 consecutive days, the conditioning phase for the cocaine-paired groups and cocaine non-paired groups began, consisting of eight subsequent daily sessions. For both groups, cocaine (10 mg / kg) or saline injections were administered on alternate days. For the cocaine-paired groups, rats were immediately placed in one of the two compartments for 30 min with the door in place restricting a z transformation followed by z test and anova followed by Student-Newman-Keuls' post hoc test. Gene expression profile was assessed 24 h after the last conditioning session that corresponded to 48 h after last cocaine exposure, when drug has been eliminated from the body and transient transcriptional changes are likely to be minimal. Therefore, changes in gene expression at this time-point are likely to reflect longer lasting adaptations that may account for maintenance of cocaine-induced memories. The complete lists of normalized gene expression values for the hippocampus of saline-treated, cocaine non-paired and cocaine-paired groups are presented. Analyses revealed that 214 transcripts were differentially regulated in the hippocampus of cocaine-paired rats vs. non-paired and saline-treated controls. Cocaine-induced conditioned place preference caused significant increases in the expression of 151 genes and caused decreases in the expression of 63 genes. (NIF Table ID 130.1 [83])
Authors:
Krasnova IN, Li SM, Wood WH, McCoy MT, Prabhu VV, Becker KG, Katz JL, Cadet JL
Chronic cocaine - Cocaine-paired (conditioned place preference) vs. Control (saline or cocaine-non-paired) DNA microarray All genes on microarray presented After the pre-conditioning phase where animals were allowed access to either compartment for 15 minutes for 4 consecutive days, the conditioning phase for the cocaine-paired groups and cocaine non-paired groups began, consisting of eight subsequent daily sessions. For both groups, cocaine (10 mg / kg) or saline injections were administered on alternate days. For the cocaine-paired groups, rats were immediately placed in one of the two compartments for 30 min with the door in place restricting a z transformation followed by z test and anova followed by Student-Newman-Keuls' post hoc test. Gene expression profile was assessed 24 h after the last conditioning session that corresponded to 48 h after last cocaine exposure, when drug has been eliminated from the body and transient transcriptional changes are likely to be minimal. Therefore, changes in gene expression at this time-point are likely to reflect longer lasting adaptations that may account for maintenance of cocaine-induced memories. The complete lists of normalized gene expression values for the frontal cortex of saline-treated, cocaine non-paired and cocaine-paired groups are presented. Differences in the expression of 39 transcripts in the frontal cortex were related to the conditioned place preference paradigm. These include increases in the level of 22 genes and decreases in 17 genes. (NIF Table ID 130.3 [83.5])
Authors:
Krasnova IN, Li SM, Wood WH, McCoy MT, Prabhu VV, Becker KG, Katz JL, Cadet JL
Genes associated with Homo sapiens that interact with the MeSH term 'Azaguanine' (D001375). Incorporates data from 134 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 'Cholesterol' (D002784). 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 Mesocricetus auratus that interact with the MeSH term 'Cholesterol, Dietary' (D002791). Incorporates data from 128 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 'Coumestrol' (D003375). 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 'Dexamethasone' (D003907). Incorporates data from 14 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 'Diclofenac' (D004008). Incorporates data from 4 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
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