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 Circulating vasoactive peptide levels. The EFO term vasoactive peptide 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:
N Verweij, H Mahmud, I Mateo Leach, RA de Boer, FP Brouwers, H Yu, FW Asselbergs, J Struck, SJ Bakker, RT Gansevoort, PB Munroe, HL Hillege, DJ van Veldhuisen, WH van Gilst, HH Silljé, P van der Harst
Dynamic and kinetic mechanisms of exogenous chemical and drug ABSORPTION; BIOLOGICAL TRANSPORT; TISSUE DISTRIBUTION; BIOTRANSFORMATION; elimination; and TOXICOLOGY as a function of dosage, and rate of METABOLISM. It includes toxicokinetics, the pharmacokinetic mechanism of the toxic effects of a substance. ADME and ADMET are short-hand abbreviations for absorption, distribution, metabolism, elimination and toxicology.
Generated by gene2mesh v. 1.1.1
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 Systolic blood pressure. The EFO term systolic blood pressure 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:
GB Ehret, PB Munroe, KM Rice, M Bochud, AD Johnson, DI Chasman, AV Smith, MD Tobin, GC Verwoert, SJ Hwang, V Pihur, P Vollenweider, PF O'Reilly, N Amin, JL Bragg-Gresham, A Teumer, NL Glazer, L Launer, JH Zhao, Y Aulchenko, S Heath, S Sõber, A Parsa, J Luan, P Arora, A Dehghan, F Zhang, G Lucas, AA Hicks, AU Jackson, JF Peden, T Tanaka, SH Wild, I Rudan, W Igl, Y Milaneschi, AN Parker, C Fava, JC Chambers, ER Fox, M Kumari, MJ Go, P van der Harst, WH Kao, M Sjögren, DG Vinay, M Alexander, Y Tabara, S Shaw-Hawkins, PH Whincup, Y Liu, G Shi, J Kuusisto, B Tayo, M Seielstad, X Sim, KD Nguyen, T Lehtimäki, G Matullo, Y Wu, TR Gaunt, NC Onland-Moret, MN Cooper, CG Platou, E Org, R Hardy, S Dahgam, J Palmen, V Vitart, PS Braund, T Kuznetsova, CS Uiterwaal, A Adeyemo, W Palmas, H Campbell, B Ludwig, M Tomaszewski, I Tzoulaki, ND Palmer, T Aspelund, M Garcia, YP Chang, JR O'Connell, NI Steinle, DE Grobbee, DE Arking, SL Kardia, AC Morrison, D Hernandez, S Najjar, WL McArdle, D Hadley, MJ Brown, JM Connell, AD Hingorani, IN Day, DA Lawlor, JP Beilby, RW Lawrence, R Clarke, JC Hopewell, H Ongen, AW Dreisbach, Y Li, JH Young, JC Bis, M Kähönen, J Viikari, LS Adair, NR Lee, MH Chen, M Olden, C Pattaro, JA Bolton, A Köttgen, S Bergmann, V Mooser, N Chaturvedi, TM Frayling, M Islam, TH Jafar, J Erdmann, SR Kulkarni, SR Bornstein, J Grässler, L Groop, BF Voight, J Kettunen, P Howard, A Taylor, S Guarrera, F Ricceri, V Emilsson, A Plump, I Barroso, KT Khaw, AB Weder, SC Hunt, YV Sun, RN Bergman, FS Collins, LL Bonnycastle, LJ Scott, HM Stringham, L Peltonen, M Perola, E Vartiainen, SM Brand, JA Staessen, TJ Wang, PR Burton, M Soler Artigas, Y Dong, H Snieder, X Wang, H Zhu, KK Lohman, ME Rudock, SR Heckbert, NL Smith, KL Wiggins, A Doumatey, D Shriner, G Veldre, M Viigimaa, S Kinra, D Prabhakaran, V Tripathy, CD Langefeld, A Rosengren, DS Thelle, AM Corsi, A Singleton, T Forrester, G Hilton, CA McKenzie, T Salako, N Iwai, Y Kita, T Ogihara, T Ohkubo, T Okamura, H Ueshima, S Umemura, S Eyheramendy, T Meitinger, HE Wichmann, YS Cho, HL Kim, JY Lee, J Scott, JS Sehmi, W Zhang, B Hedblad, P Nilsson, GD Smith, A Wong, N Narisu, A Stančáková, LJ Raffel, J Yao, S Kathiresan, CJ O'Donnell, SM Schwartz, MA Ikram, WT Longstreth, TH Mosley, S Seshadri, NR Shrine, LV Wain, MA Morken, AJ Swift, J Laitinen, I Prokopenko, P Zitting, JA Cooper, SE Humphries, J Danesh, A Rasheed, A Goel, A Hamsten, H Watkins, SJ Bakker, WH van Gilst, CS Janipalli, KR Mani, CS Yajnik, A Hofman, FU Mattace-Raso, BA Oostra, A Demirkan, A Isaacs, F Rivadeneira, EG Lakatta, M Orru, A Scuteri, M Ala-Korpela, AJ Kangas, LP Lyytikäinen, P Soininen, T Tukiainen, P Würtz, RT Ong, M Dörr, HK Kroemer, U Völker, H Völzke, P Galan, S Hercberg, M Lathrop, D Zelenika, P Deloukas, M Mangino, TD Spector, G Zhai, JF Meschia, MA Nalls, P Sharma, J Terzic, MV Kumar, M Denniff, E Zukowska-Szczechowska, LE Wagenknecht, FG Fowkes, FJ Charchar, PE Schwarz, C Hayward, X Guo, C Rotimi, ML Bots, E Brand, NJ Samani, O Polasek, PJ Talmud, F Nyberg, D Kuh, M Laan, K Hveem, LJ Palmer, YT van der Schouw, JP Casas, KL Mohlke, P Vineis, O Raitakari, SK Ganesh, TY Wong, ES Tai, RS Cooper, M Laakso, DC Rao, TB Harris, RW Morris, AF Dominiczak, M Kivimaki, MG Marmot, T Miki, D Saleheen, GR Chandak, J Coresh, G Navis, V Salomaa, BG Han, X Zhu, JS Kooner, O Melander, PM Ridker, S Bandinelli, UB Gyllensten, AF Wright, JF Wilson, L Ferrucci, M Farrall, J Tuomilehto, PP Pramstaller, R Elosua, N Soranzo, EJ Sijbrands, D Altshuler, RJ Loos, AR Shuldiner, C Gieger, P Meneton, AG Uitterlinden, NJ Wareham, V Gudnason, JI Rotter, R Rettig, M Uda, DP Strachan, JC Witteman, AL Hartikainen, JS Beckmann, E Boerwinkle, RS Vasan, M Boehnke, MG Larson, MR Järvelin, BM Psaty, GR Abecasis, A Chakravarti, P Elliott, CM van Duijn, C Newton-Cheh, D Levy, MJ Caulfield, T Johnson
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 Diastolic blood pressure. The EFO term diastolic blood pressure 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:
GB Ehret, PB Munroe, KM Rice, M Bochud, AD Johnson, DI Chasman, AV Smith, MD Tobin, GC Verwoert, SJ Hwang, V Pihur, P Vollenweider, PF O'Reilly, N Amin, JL Bragg-Gresham, A Teumer, NL Glazer, L Launer, JH Zhao, Y Aulchenko, S Heath, S Sõber, A Parsa, J Luan, P Arora, A Dehghan, F Zhang, G Lucas, AA Hicks, AU Jackson, JF Peden, T Tanaka, SH Wild, I Rudan, W Igl, Y Milaneschi, AN Parker, C Fava, JC Chambers, ER Fox, M Kumari, MJ Go, P van der Harst, WH Kao, M Sjögren, DG Vinay, M Alexander, Y Tabara, S Shaw-Hawkins, PH Whincup, Y Liu, G Shi, J Kuusisto, B Tayo, M Seielstad, X Sim, KD Nguyen, T Lehtimäki, G Matullo, Y Wu, TR Gaunt, NC Onland-Moret, MN Cooper, CG Platou, E Org, R Hardy, S Dahgam, J Palmen, V Vitart, PS Braund, T Kuznetsova, CS Uiterwaal, A Adeyemo, W Palmas, H Campbell, B Ludwig, M Tomaszewski, I Tzoulaki, ND Palmer, T Aspelund, M Garcia, YP Chang, JR O'Connell, NI Steinle, DE Grobbee, DE Arking, SL Kardia, AC Morrison, D Hernandez, S Najjar, WL McArdle, D Hadley, MJ Brown, JM Connell, AD Hingorani, IN Day, DA Lawlor, JP Beilby, RW Lawrence, R Clarke, JC Hopewell, H Ongen, AW Dreisbach, Y Li, JH Young, JC Bis, M Kähönen, J Viikari, LS Adair, NR Lee, MH Chen, M Olden, C Pattaro, JA Bolton, A Köttgen, S Bergmann, V Mooser, N Chaturvedi, TM Frayling, M Islam, TH Jafar, J Erdmann, SR Kulkarni, SR Bornstein, J Grässler, L Groop, BF Voight, J Kettunen, P Howard, A Taylor, S Guarrera, F Ricceri, V Emilsson, A Plump, I Barroso, KT Khaw, AB Weder, SC Hunt, YV Sun, RN Bergman, FS Collins, LL Bonnycastle, LJ Scott, HM Stringham, L Peltonen, M Perola, E Vartiainen, SM Brand, JA Staessen, TJ Wang, PR Burton, M Soler Artigas, Y Dong, H Snieder, X Wang, H Zhu, KK Lohman, ME Rudock, SR Heckbert, NL Smith, KL Wiggins, A Doumatey, D Shriner, G Veldre, M Viigimaa, S Kinra, D Prabhakaran, V Tripathy, CD Langefeld, A Rosengren, DS Thelle, AM Corsi, A Singleton, T Forrester, G Hilton, CA McKenzie, T Salako, N Iwai, Y Kita, T Ogihara, T Ohkubo, T Okamura, H Ueshima, S Umemura, S Eyheramendy, T Meitinger, HE Wichmann, YS Cho, HL Kim, JY Lee, J Scott, JS Sehmi, W Zhang, B Hedblad, P Nilsson, GD Smith, A Wong, N Narisu, A Stančáková, LJ Raffel, J Yao, S Kathiresan, CJ O'Donnell, SM Schwartz, MA Ikram, WT Longstreth, TH Mosley, S Seshadri, NR Shrine, LV Wain, MA Morken, AJ Swift, J Laitinen, I Prokopenko, P Zitting, JA Cooper, SE Humphries, J Danesh, A Rasheed, A Goel, A Hamsten, H Watkins, SJ Bakker, WH van Gilst, CS Janipalli, KR Mani, CS Yajnik, A Hofman, FU Mattace-Raso, BA Oostra, A Demirkan, A Isaacs, F Rivadeneira, EG Lakatta, M Orru, A Scuteri, M Ala-Korpela, AJ Kangas, LP Lyytikäinen, P Soininen, T Tukiainen, P Würtz, RT Ong, M Dörr, HK Kroemer, U Völker, H Völzke, P Galan, S Hercberg, M Lathrop, D Zelenika, P Deloukas, M Mangino, TD Spector, G Zhai, JF Meschia, MA Nalls, P Sharma, J Terzic, MV Kumar, M Denniff, E Zukowska-Szczechowska, LE Wagenknecht, FG Fowkes, FJ Charchar, PE Schwarz, C Hayward, X Guo, C Rotimi, ML Bots, E Brand, NJ Samani, O Polasek, PJ Talmud, F Nyberg, D Kuh, M Laan, K Hveem, LJ Palmer, YT van der Schouw, JP Casas, KL Mohlke, P Vineis, O Raitakari, SK Ganesh, TY Wong, ES Tai, RS Cooper, M Laakso, DC Rao, TB Harris, RW Morris, AF Dominiczak, M Kivimaki, MG Marmot, T Miki, D Saleheen, GR Chandak, J Coresh, G Navis, V Salomaa, BG Han, X Zhu, JS Kooner, O Melander, PM Ridker, S Bandinelli, UB Gyllensten, AF Wright, JF Wilson, L Ferrucci, M Farrall, J Tuomilehto, PP Pramstaller, R Elosua, N Soranzo, EJ Sijbrands, D Altshuler, RJ Loos, AR Shuldiner, C Gieger, P Meneton, AG Uitterlinden, NJ Wareham, V Gudnason, JI Rotter, R Rettig, M Uda, DP Strachan, JC Witteman, AL Hartikainen, JS Beckmann, E Boerwinkle, RS Vasan, M Boehnke, MG Larson, MR Järvelin, BM Psaty, GR Abecasis, A Chakravarti, P Elliott, CM van Duijn, C Newton-Cheh, D Levy, MJ Caulfield, T Johnson
Gene expression changes in the post-mortem nucleus accumbens of chronic heroin abusers. Overall, little overlap in gene expression profiles was seen between the two drug-abusing cohorts: out of the approximately 39,000 transcripts investigated, the abundance of only 25 was significantly changed in both cocaine and heroin abusers, with nearly one-half of these being altered in opposite directions. 1050 Transcripts had different in abundance between the majority of heroin subjects and their matched controls.
Nrf2 binds to CREB Binding Protein for enhanced transcription activating activity. Cigarette Smoke (CS)-induced oxidative stress has been associated with the expression of Nrf2 transcription-dependent antioxidant and cytoprotective genes [40]. Nrf2 knockout and Wild-type mice were exposed to CS and Air. The genes listed here are up-regulated in both groups, suggesting that their transcriptional regulation is Nrf2-independent
Nrf2 binds to CREB Binding Protein for enhanced transcription activating activity. Cigarette Smoke (CS)-induced oxidative stress has been associated with the expression of Nrf2 transcription-dependent antioxidant and cytoprotective genes. Nrf2 knockout and Wild-type mice were exposed to CS and Air. The genes listed here are up-regulated in both groups, suggesting that their transcriptional regulation is Nrf2-independent.
Striatum Gene Expression Correlates for MDMA_ACT_SAL_2 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The MDMA_ACT_SAL_2 measures Locomotor activity after second saline treatment. 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
FC of the probe sets encoding AMP genes that were significant in one of the performed comparative analyses in UC
Authors:
Arijs I, De Hertogh G, Lemaire K, Quintens R, Van Lommel L, Van Steen K, Leemans P, Cleynen I, Van Assche G, Vermeire S, Geboes K, Schuit F, Rutgeerts P
FC of the probe sets encoding AMP genes that were significant in one of the performed comparative analyses in CD
Authors:
Arijs I, De Hertogh G, Lemaire K, Quintens R, Van Lommel L, Van Steen K, Leemans P, Cleynen I, Van Assche G, Vermeire S, Geboes K, Schuit F, Rutgeerts P
alcohol preference locus 11, male specific at D7Mit19 ((Tyr) spans 69.5-119.5 Mbp (NCBI Build 37) on Chr7. Has a preference correlation of 0.555, a LOD of 1.91 with a p < 0.003. 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 nicotine sensitivity on Chr7 at D7Mit66 (116.91 Mbp , Build 37)
Description:
nicotine sensitivity spans 91.91 - 141.91 Mbp (NCBI Build 37) on Chr7. 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 alcohol preference locus on Chr7 at D7Mit105 (126.73 Mbp , Build 37)
Description:
alcohol preference locus spans 101.73 - 151.73 Mbp (NCBI Build 37) on Chr7. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
alcohol preference locus 14, female specific at D7Mit105 with a LOD score of 1.84 (p < 0.004) spans and preference correlation of 0.591 101.73 - 151.73 Mbp (NCBI Build 37) on Chr7. 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 home cage activity on Chr7 at D7Mit12 (129.57 Mbp , Build 37)
Description:
METH responses for home cage activity spans 104.57 - 154.57 Mbp (NCBI Build 37) on Chr7. 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 Chr7 at Xmv76 (137.02 Mbp , Build 37)
Description:
METH responses for body temperature spans 112.02 - 162.02 Mbp (NCBI Build 37) on Chr7. 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 '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 Oryctolagus cuniculus that interact with the MeSH term 'Ionomycin' (D015759). 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 'Fluorouracil' (D005472). Incorporates data from 99 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.
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