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 glucose-related traits. 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.
Authors:
J Dupuis, C Langenberg, I Prokopenko, R Saxena, N Soranzo, AU Jackson, E Wheeler, NL Glazer, N Bouatia-Naji, AL Gloyn, CM Lindgren, R Mägi, AP Morris, J Randall, T Johnson, P Elliott, D Rybin, G Thorleifsson, V Steinthorsdottir, P Henneman, H Grallert, A Dehghan, JJ Hottenga, CS Franklin, P Navarro, K Song, A Goel, JR Perry, JM Egan, T Lajunen, N Grarup, T Sparsø, A Doney, BF Voight, HM Stringham, M Li, S Kanoni, P Shrader, C Cavalcanti-Proença, M Kumari, L Qi, NJ Timpson, C Gieger, C Zabena, G Rocheleau, E Ingelsson, P An, J O'Connell, J Luan, A Elliott, SA McCarroll, F Payne, RM Roccasecca, F Pattou, P Sethupathy, K Ardlie, Y Ariyurek, B Balkau, P Barter, JP Beilby, Y Ben-Shlomo, R Benediktsson, AJ Bennett, S Bergmann, M Bochud, E Boerwinkle, A Bonnefond, LL Bonnycastle, K Borch-Johnsen, Y Böttcher, E Brunner, SJ Bumpstead, G Charpentier, YD Chen, P Chines, R Clarke, LJ Coin, MN Cooper, M Cornelis, G Crawford, L Crisponi, IN Day, EJ de Geus, J Delplanque, C Dina, MR Erdos, AC Fedson, A Fischer-Rosinsky, NG Forouhi, CS Fox, R Frants, MG Franzosi, P Galan, MO Goodarzi, J Graessler, CJ Groves, S Grundy, R Gwilliam, U Gyllensten, S Hadjadj, G Hallmans, N Hammond, X Han, AL Hartikainen, N Hassanali, C Hayward, SC Heath, S Hercberg, C Herder, AA Hicks, DR Hillman, AD Hingorani, A Hofman, J Hui, J Hung, B Isomaa, PR Johnson, T Jørgensen, A Jula, M Kaakinen, J Kaprio, YA Kesaniemi, M Kivimaki, B Knight, S Koskinen, P Kovacs, KO Kyvik, GM Lathrop, DA Lawlor, O Le Bacquer, C Lecoeur, Y Li, V Lyssenko, R Mahley, M Mangino, AK Manning, MT MartÃnez-Larrad, JB McAteer, LJ McCulloch, R McPherson, C Meisinger, D Melzer, D Meyre, BD Mitchell, MA Morken, S Mukherjee, S Naitza, N Narisu, MJ Neville, BA Oostra, M Orrù, R Pakyz, CN Palmer, G Paolisso, C Pattaro, D Pearson, JF Peden, NL Pedersen, M Perola, AF Pfeiffer, I Pichler, O Polasek, D Posthuma, SC Potter, A Pouta, MA Province, BM Psaty, W Rathmann, NW Rayner, K Rice, S Ripatti, F Rivadeneira, M Roden, O Rolandsson, A Sandbaek, M Sandhu, S Sanna, AA Sayer, P Scheet, LJ Scott, U Seedorf, SJ Sharp, B Shields, G Sigurethsson, EJ Sijbrands, A Silveira, L Simpson, A Singleton, NL Smith, U Sovio, A Swift, H Syddall, AC Syvänen, T Tanaka, B Thorand, J Tichet, A Tönjes, T Tuomi, AG Uitterlinden, KW van Dijk, M van Hoek, D Varma, S Visvikis-Siest, V Vitart, N Vogelzangs, G Waeber, PJ Wagner, A Walley, GB Walters, KL Ward, H Watkins, MN Weedon, SH Wild, G Willemsen, JC Witteman, JW Yarnell, E Zeggini, D Zelenika, B Zethelius, G Zhai, JH Zhao, MC Zillikens, IB Borecki, RJ Loos, P Meneton, PK Magnusson, DM Nathan, GH Williams, AT Hattersley, K Silander, V Salomaa, GD Smith, SR Bornstein, P Schwarz, J Spranger, F Karpe, AR Shuldiner, C Cooper, GV Dedoussis, M Serrano-RÃos, AD Morris, L Lind, LJ Palmer, FB Hu, PW Franks, S Ebrahim, M Marmot, WH Kao, JS Pankow, MJ Sampson, J Kuusisto, M Laakso, T Hansen, O Pedersen, PP Pramstaller, HE Wichmann, T Illig, I Rudan, AF Wright, M Stumvoll, H Campbell, JF Wilson, RN Bergman, TA Buchanan, FS Collins, KL Mohlke, J Tuomilehto, TT Valle, D Altshuler, JI Rotter, DS Siscovick, BW Penninx, DI Boomsma, P Deloukas, TD Spector, TM Frayling, L Ferrucci, A Kong, U Thorsteinsdottir, K Stefansson, CM van Duijn, YS Aulchenko, A Cao, A Scuteri, D Schlessinger, M Uda, A Ruokonen, MR Jarvelin, DM Waterworth, P Vollenweider, L Peltonen, V Mooser, GR Abecasis, NJ Wareham, R Sladek, P Froguel, RM Watanabe, JB Meigs, L Groop, M Boehnke, MI McCarthy, JC Florez, I Barroso
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 glucose-related traits. The EFO term HOMA-B 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 Dupuis, C Langenberg, I Prokopenko, R Saxena, N Soranzo, AU Jackson, E Wheeler, NL Glazer, N Bouatia-Naji, AL Gloyn, CM Lindgren, R Mägi, AP Morris, J Randall, T Johnson, P Elliott, D Rybin, G Thorleifsson, V Steinthorsdottir, P Henneman, H Grallert, A Dehghan, JJ Hottenga, CS Franklin, P Navarro, K Song, A Goel, JR Perry, JM Egan, T Lajunen, N Grarup, T Sparsø, A Doney, BF Voight, HM Stringham, M Li, S Kanoni, P Shrader, C Cavalcanti-Proença, M Kumari, L Qi, NJ Timpson, C Gieger, C Zabena, G Rocheleau, E Ingelsson, P An, J O'Connell, J Luan, A Elliott, SA McCarroll, F Payne, RM Roccasecca, F Pattou, P Sethupathy, K Ardlie, Y Ariyurek, B Balkau, P Barter, JP Beilby, Y Ben-Shlomo, R Benediktsson, AJ Bennett, S Bergmann, M Bochud, E Boerwinkle, A Bonnefond, LL Bonnycastle, K Borch-Johnsen, Y Böttcher, E Brunner, SJ Bumpstead, G Charpentier, YD Chen, P Chines, R Clarke, LJ Coin, MN Cooper, M Cornelis, G Crawford, L Crisponi, IN Day, EJ de Geus, J Delplanque, C Dina, MR Erdos, AC Fedson, A Fischer-Rosinsky, NG Forouhi, CS Fox, R Frants, MG Franzosi, P Galan, MO Goodarzi, J Graessler, CJ Groves, S Grundy, R Gwilliam, U Gyllensten, S Hadjadj, G Hallmans, N Hammond, X Han, AL Hartikainen, N Hassanali, C Hayward, SC Heath, S Hercberg, C Herder, AA Hicks, DR Hillman, AD Hingorani, A Hofman, J Hui, J Hung, B Isomaa, PR Johnson, T Jørgensen, A Jula, M Kaakinen, J Kaprio, YA Kesaniemi, M Kivimaki, B Knight, S Koskinen, P Kovacs, KO Kyvik, GM Lathrop, DA Lawlor, O Le Bacquer, C Lecoeur, Y Li, V Lyssenko, R Mahley, M Mangino, AK Manning, MT MartÃnez-Larrad, JB McAteer, LJ McCulloch, R McPherson, C Meisinger, D Melzer, D Meyre, BD Mitchell, MA Morken, S Mukherjee, S Naitza, N Narisu, MJ Neville, BA Oostra, M Orrù, R Pakyz, CN Palmer, G Paolisso, C Pattaro, D Pearson, JF Peden, NL Pedersen, M Perola, AF Pfeiffer, I Pichler, O Polasek, D Posthuma, SC Potter, A Pouta, MA Province, BM Psaty, W Rathmann, NW Rayner, K Rice, S Ripatti, F Rivadeneira, M Roden, O Rolandsson, A Sandbaek, M Sandhu, S Sanna, AA Sayer, P Scheet, LJ Scott, U Seedorf, SJ Sharp, B Shields, G Sigurethsson, EJ Sijbrands, A Silveira, L Simpson, A Singleton, NL Smith, U Sovio, A Swift, H Syddall, AC Syvänen, T Tanaka, B Thorand, J Tichet, A Tönjes, T Tuomi, AG Uitterlinden, KW van Dijk, M van Hoek, D Varma, S Visvikis-Siest, V Vitart, N Vogelzangs, G Waeber, PJ Wagner, A Walley, GB Walters, KL Ward, H Watkins, MN Weedon, SH Wild, G Willemsen, JC Witteman, JW Yarnell, E Zeggini, D Zelenika, B Zethelius, G Zhai, JH Zhao, MC Zillikens, IB Borecki, RJ Loos, P Meneton, PK Magnusson, DM Nathan, GH Williams, AT Hattersley, K Silander, V Salomaa, GD Smith, SR Bornstein, P Schwarz, J Spranger, F Karpe, AR Shuldiner, C Cooper, GV Dedoussis, M Serrano-RÃos, AD Morris, L Lind, LJ Palmer, FB Hu, PW Franks, S Ebrahim, M Marmot, WH Kao, JS Pankow, MJ Sampson, J Kuusisto, M Laakso, T Hansen, O Pedersen, PP Pramstaller, HE Wichmann, T Illig, I Rudan, AF Wright, M Stumvoll, H Campbell, JF Wilson, RN Bergman, TA Buchanan, FS Collins, KL Mohlke, J Tuomilehto, TT Valle, D Altshuler, JI Rotter, DS Siscovick, BW Penninx, DI Boomsma, P Deloukas, TD Spector, TM Frayling, L Ferrucci, A Kong, U Thorsteinsdottir, K Stefansson, CM van Duijn, YS Aulchenko, A Cao, A Scuteri, D Schlessinger, M Uda, A Ruokonen, MR Jarvelin, DM Waterworth, P Vollenweider, L Peltonen, V Mooser, GR Abecasis, NJ Wareham, R Sladek, P Froguel, RM Watanabe, JB Meigs, L Groop, M Boehnke, MI McCarthy, JC Florez, I Barroso
Cerebellum Gene Expression Correlates for HOTPLATE_MEANOF2 measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The HOTPLATE_MEANOF2 measures Thermal Nociception Hot Plate Avg of 2Trials under the domain Pain. 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 VONFREYTHRESHOLDMEAN measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The VONFREYTHRESHOLDMEAN measures Mechanical Sensitivity-Von Frey Threshold under the domain Pain. 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 ADRE_RIGHT_WT measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) 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
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
These genes are a 1 class SAM significant (1% FDR) in nucleus accumbens (core + shell) for saline treated ("basal") control vs. Fyn KO mice. The list was filtered for an average Sscore >2.0 or <-2.0. Data from Farris and Miles, PLoS One, 2013.
QTL for ethanol withdrawal on Chr12 at D12Ncvs38 (14.25 Mbp , Build 37)
Description:
ethanol withdrawal spans 0.00 - 39.25 Mbp (NCBI Build 37) on Chr12. 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 differences in cocaine responsiveness on Chr12 at D12M!t2 (39.51 Mbp , Build 37)
Description:
differences in cocaine responsiveness spans 14.51 - 64.51 Mbp (NCBI Build 37) on Chr12. 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 METH responses for body temperature on Chr12 at Mox2 (45.22 Mbp , Build 37)
Description:
METH responses for body temperature spans 20.22 - 70.22 Mbp (NCBI Build 37) on Chr12. 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 cocaine induced activation on Chr12 at D12Xrf564 (55.38 Mbp , Build 37)
Description:
cocaine induced activation spans 30.38 - 80.38 Mbp (NCBI Build 37) on Chr12. 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 '8-Bromo Cyclic Adenosine Monophosphate' (D015124). Incorporates data from 233 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Ovis aries that interact with the MeSH term 'Progesterone' (D011374). 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 Gadus morhua that interact with the MeSH term 'methylmercuric chloride' (C004925). Incorporates data from 4 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 'Valproic Acid' (D014635). Incorporates data from 1238 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 'Vanadium' (D014639). Incorporates data from 5 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 'trichostatin A' (C012589). 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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