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 Urate levels. The EFO term urate 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:
A Köttgen, E Albrecht, A Teumer, V Vitart, J Krumsiek, C Hundertmark, G Pistis, D Ruggiero, CM O'Seaghdha, T Haller, Q Yang, T Tanaka, AD Johnson, Z Kutalik, AV Smith, J Shi, M Struchalin, RP Middelberg, MJ Brown, AL Gaffo, N Pirastu, G Li, C Hayward, T Zemunik, J Huffman, L Yengo, JH Zhao, A Demirkan, MF Feitosa, X Liu, G Malerba, LM Lopez, P van der Harst, X Li, ME Kleber, AA Hicks, IM Nolte, A Johansson, F Murgia, SH Wild, SJ Bakker, JF Peden, A Dehghan, M Steri, A Tenesa, V Lagou, P Salo, M Mangino, LM Rose, T Lehtimäki, OM Woodward, Y Okada, A Tin, C Müller, C Oldmeadow, M Putku, D Czamara, P Kraft, L Frogheri, GA Thun, A Grotevendt, GK Gislason, TB Harris, LJ Launer, P McArdle, AR Shuldiner, E Boerwinkle, J Coresh, H Schmidt, M Schallert, NG Martin, GW Montgomery, M Kubo, Y Nakamura, T Tanaka, PB Munroe, NJ Samani, DR Jacobs, K Liu, P D'Adamo, S Ulivi, JI Rotter, BM Psaty, P Vollenweider, G Waeber, S Campbell, O Devuyst, P Navarro, I Kolcic, N Hastie, B Balkau, P Froguel, T Esko, A Salumets, KT Khaw, C Langenberg, NJ Wareham, A Isaacs, A Kraja, Q Zhang, PS Wild, RJ Scott, EG Holliday, E Org, M Viigimaa, S Bandinelli, JE Metter, A Lupo, E Trabetti, R Sorice, A Döring, E Lattka, K Strauch, F Theis, M Waldenberger, HE Wichmann, G Davies, AJ Gow, M Bruinenberg, RP Stolk, JS Kooner, W Zhang, BR Winkelmann, BO Boehm, S Lucae, BW Penninx, JH Smit, G Curhan, P Mudgal, RM Plenge, L Portas, I Persico, M Kirin, JF Wilson, I Mateo Leach, WH van Gilst, A Goel, H Ongen, A Hofman, F Rivadeneira, AG Uitterlinden, M Imboden, A von Eckardstein, F Cucca, R Nagaraja, MG Piras, M Nauck, C Schurmann, K Budde, F Ernst, SM Farrington, E Theodoratou, I Prokopenko, M Stumvoll, A Jula, M Perola, V Salomaa, SY Shin, TD Spector, C Sala, PM Ridker, M Kähönen, J Viikari, C Hengstenberg, CP Nelson, JF Meschia, MA Nalls, P Sharma, AB Singleton, N Kamatani, T Zeller, M Burnier, J Attia, M Laan, N Klopp, HL Hillege, S Kloiber, H Choi, M Pirastu, S Tore, NM Probst-Hensch, H Völzke, V Gudnason, A Parsa, R Schmidt, JB Whitfield, M Fornage, P Gasparini, DS Siscovick, O Polašek, H Campbell, I Rudan, N Bouatia-Naji, A Metspalu, RJ Loos, CM van Duijn, IB Borecki, L Ferrucci, G Gambaro, IJ Deary, BH Wolffenbuttel, JC Chambers, W März, PP Pramstaller, H Snieder, U Gyllensten, AF Wright, G Navis, H Watkins, JC Witteman, S Sanna, S Schipf, MG Dunlop, A Tönjes, S Ripatti, N Soranzo, D Toniolo, DI Chasman, O Raitakari, WH Kao, M Ciullo, CS Fox, M Caulfield, M Bochud, C Gieger
Striatum Gene Expression Correlates for OF_DIST_15_20 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The OF_DIST_15_20 measures Open Field - Total distance traveled 15-20 minutes 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
Cerebellum Gene Expression Correlates for PTOSIS measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The PTOSIS measures Morphine - Severity of ptosis 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
QTL for cocaine related behavior on Chr5 at D5Mit7 (103.64 Mbp , Build 37)
Description:
cocaine related behavior spans 78.64 - 128.64 Mbp (NCBI Build 37) on Chr5. 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 Chr5 at Cyp3 (108.78 Mbp , Build 37)
Description:
differences in cocaine responsiveness spans 83.78 - 133.78 Mbp (NCBI Build 37) on Chr5. 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 chewing on Chr5 at D5Mit10 (111.96 Mbp , Build 37)
Description:
METH responses for chewing spans 86.96 - 136.96 Mbp (NCBI Build 37) on Chr5. 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 climbing on Chr5 at D5Byu4 (129.78 Mbp , Build 37)
Description:
METH responses for climbing spans 104.78 - 154.78 Mbp (NCBI Build 37) on Chr5. 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 climbing on Chr5 at Ache (142.47 Mbp , Build 37)
Description:
METH responses for climbing spans 117.47 - 167.47 Mbp (NCBI Build 37) on Chr5. 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 'Uric Acid' (D014527). Incorporates data from 7 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 'rosiglitazone' (C089730). 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 'Oxygen' (D010100). Incorporates data from 8 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 'Plant Extracts' (D010936). Incorporates data from 489 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Rats in separate cage with free choice of water or 10% (v/v) of ethanol; consumption scores (grams/kg/day) were averaged; the amounts of ethanol consumed every 3 days over three weeks. Additive QTL. Variance 4, LOD 4.7 Peak Marker: D12Rat18 spans D12Rat93 (29675888) - D12Mgh10 (39018219). Strains were HAD1, LAD1
Authors:
Foroud T, Bice P, Castelluccio P, Bo R, Miller L, Ritchotte A, Lumeng L, Li TK, Carr LG
Rats in separate cage with free choice of water or 10% (v/v) of ethanol; consumption scores (grams/kg/day) were averaged; the amounts of ethanol consumed every 3 days over three weeks. Additive QTL. LOD 2.2 Peak Marker: D12Rat18 spans D12Mit2(20932559) - D12Mgh9(41447890). Strains were HAD1, LAD1
Authors:
Carr LG, Habegger K, Spence J, Ritchotte A, Liu L, Lumeng L, Li TK, Foroud T
Average rotarod training latency Chr# 5 rs13478110 (9741228) with right flanking marker rs13478092(3595407) and left marker rs3718776 (150393227). This was mapped in 300 + (b6x129)F2 mice.
QTL associated with activity-distance traveled 3. This interval was obtained by using a fixed interval width of 25 Mbp around the peak marker (113601539)
QTL associated with autoimmune extremity vasculitis in MRL mice 2. This interval was obtained by using a fixed interval width of 25 Mbp around the peak marker (119175776)
Authors:
Yamada A, Miyazaki T, Lu LM, Ono M, Ito MR, Terada M, Mori S, Hata K, Nozaki Y, Nakatsuru S, Nakamura Y, Onji M, Nose M
QTL associated with B.burgdorferi-associated arthritis 2. This interval was obtained by using a fixed interval width of 25 Mbp around the peak marker (120256981)
Authors:
Ma Y, Miller JC, Crandall H, Larsen ET, Dunn DM, Weiss RB, Subramanian M, Weis JH, Zachary JF, Teuscher C, Weis JJ
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