Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "CRD-mediated mRNA stability complex", which is defined as "A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, it may consist of IGF2BP1, HNRNPU, SYNCRIP/HNRNPQ, YBX1, and DHX9." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
"A protein complex that binds to, and promotes stabilization of, mRNA molecules containing the coding region instability determinant (CRD). In human, IGF2BP1 and at least four additional proteins: HNRNPU, SYNCRIP, YBX1, and DHX9." [GOC:mah, PMID:19029303]
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 Primary tooth development (number of teeth). The EFO term odontogenesis 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:
D Pillas, CJ Hoggart, DM Evans, PF O'Reilly, K Sipilä, R Lähdesmäki, IY Millwood, M Kaakinen, G Netuveli, D Blane, P Charoen, U Sovio, A Pouta, N Freimer, AL Hartikainen, J Laitinen, S Vaara, B Glaser, P Crawford, NJ Timpson, SM Ring, G Deng, W Zhang, MI McCarthy, P Deloukas, L Peltonen, P Elliott, LJ Coin, GD Smith, MR Jarvelin
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 Body fat percentage. The EFO term body fat percentage 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:
Y Lu, FR Day, S Gustafsson, ML Buchkovich, J Na, V Bataille, DL Cousminer, Z Dastani, AW Drong, T Esko, DM Evans, M Falchi, MF Feitosa, T Ferreira, ÅK Hedman, R Haring, PG Hysi, MM Iles, AE Justice, S Kanoni, V Lagou, R Li, X Li, A Locke, C Lu, R Mägi, JR Perry, TH Pers, Q Qi, M Sanna, EM Schmidt, WR Scott, D Shungin, A Teumer, AA Vinkhuyzen, RW Walker, HJ Westra, M Zhang, W Zhang, JH Zhao, Z Zhu, U Afzal, TS Ahluwalia, SJ Bakker, C Bellis, A Bonnefond, K Borodulin, AS Buchman, T Cederholm, AC Choh, HJ Choi, JE Curran, LC de Groot, PL De Jager, RA Dhonukshe-Rutten, AW Enneman, E Eury, DS Evans, T Forsen, N Friedrich, F Fumeron, ME Garcia, S Gärtner, BG Han, AS Havulinna, C Hayward, D Hernandez, H Hillege, T Ittermann, JW Kent, I Kolcic, T Laatikainen, J Lahti, I Mateo Leach, CG Lee, JY Lee, T Liu, Y Liu, S Lobbens, M Loh, LP Lyytikäinen, C Medina-Gomez, K Michaëlsson, MA Nalls, CM Nielson, L Oozageer, L Pascoe, L Paternoster, O Polašek, S Ripatti, MA Sarzynski, CS Shin, NS Narančić, D Spira, P Srikanth, E Steinhagen-Thiessen, YJ Sung, KM Swart, L Taittonen, T Tanaka, E Tikkanen, N van der Velde, NM van Schoor, N Verweij, AF Wright, L Yu, JM Zmuda, N Eklund, T Forrester, N Grarup, AU Jackson, K Kristiansson, T Kuulasmaa, J Kuusisto, P Lichtner, J Luan, A Mahajan, S Männistö, CD Palmer, JS Ried, RA Scott, A Stancáková, PJ Wagner, A Demirkan, A Döring, V Gudnason, DP Kiel, B Kühnel, M Mangino, B Mcknight, C Menni, JR O'Connell, BA Oostra, AR Shuldiner, K Song, L Vandenput, CM van Duijn, P Vollenweider, CC White, M Boehnke, Y Boettcher, RS Cooper, NG Forouhi, C Gieger, H Grallert, A Hingorani, T Jørgensen, P Jousilahti, M Kivimaki, M Kumari, M Laakso, C Langenberg, A Linneberg, A Luke, CA Mckenzie, A Palotie, O Pedersen, A Peters, K Strauch, BO Tayo, NJ Wareham, DA Bennett, L Bertram, J Blangero, M Blüher, C Bouchard, H Campbell, NH Cho, SR Cummings, SA Czerwinski, I Demuth, R Eckardt, JG Eriksson, L Ferrucci, OH Franco, P Froguel, RT Gansevoort, T Hansen, TB Harris, N Hastie, M Heliövaara, A Hofman, JM Jordan, A Jula, M Kähönen, E Kajantie, PB Knekt, S Koskinen, P Kovacs, T Lehtimäki, L Lind, Y Liu, ES Orwoll, C Osmond, M Perola, L Pérusse, OT Raitakari, T Rankinen, DC Rao, TK Rice, F Rivadeneira, I Rudan, V Salomaa, TI Sørensen, M Stumvoll, A Tönjes, B Towne, GJ Tranah, A Tremblay, AG Uitterlinden, P van der Harst, E Vartiainen, JS Viikari, V Vitart, MC Vohl, H Völzke, M Walker, H Wallaschofski, S Wild, JF Wilson, L Yengo, DT Bishop, IB Borecki, JC Chambers, LA Cupples, A Dehghan, P Deloukas, G Fatemifar, C Fox, TS Furey, L Franke, J Han, DJ Hunter, J Karjalainen, F Karpe, RC Kaplan, JS Kooner, MI McCarthy, JM Murabito, AP Morris, JA Bishop, KE North, C Ohlsson, KK Ong, I Prokopenko, JB Richards, EE Schadt, TD Spector, E Widén, CJ Willer, J Yang, E Ingelsson, KL Mohlke, JN Hirschhorn, JA Pospisilik, MC Zillikens, C Lindgren, TO Kilpeläinen, RJ Loos
Using a zebrafish model, study demonstrates that adult zebrafish show dose-dependent acute conditioned place preference reinforcement response to ethanol or nicotine. To analyze gene expression results, microarray analysis was performed using whole brain samples and 153 genes affecting ethanol and nicotine dependence were found. This gene set comprises 140 genes showing 1.5-fold greater changes in expression in both ethanol-treated and nicotine-treated animals compared with control animals.
This gene set comprises 102 genes showing twofold changes in expression in both ethanol-treated and nicotine-treated animals compared with control animals. Background: Using a zebrafish model, study demonstrates that adult zebrafish show a dose-dependent acute conditioned place preference (CPP) reinforcement response to ethanol or nicotine. To analyze gene expression results, microarray analysis was performed using whole brain samples and 153 genes that affect ethanol and nicotine dependence were found.
Gene set comprises 32 smoking cessation genes. Background: Using results from genome wide association studies of nicotine dependent individuals who were successful in abstaining from cigarette smoking, study nominates genes important in nicotine dependence and in smoking cessation. Results were obtained using SNP allele frequency assessments of DNA prepared from nicotine-dependent European-American smoking cessation trial participants and control individuals.
Authors:
Uhl GR, Liu QR, Drgon T, Johnson C, Walther D, Rose JE
Striatum Gene Expression Correlates for TAILCLIP_LAT_SEC measured in BXD RI Females obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The TAILCLIP_LAT_SEC measures Mechanical Nociception - Tail Clip Test 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 TAILCLIP_LAT_SEC measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The TAILCLIP_LAT_SEC measures Mechanical Nociception - Tail Clip Test 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
Whole Brain Gene Expression Correlates for OF_CORNER_TIME_PCT measured in BXD RI Females obtained using INIA Brain mRNA M430 (Jun06) RMA. The OF_CORNER_TIME_PCT measures Open Field - Total time in corners 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
Whole Brain Gene Expression Correlates for OF_CORNER_TIME_PCT measured in BXD RI Females obtained using INIA Brain mRNA M430 (Jun06) RMA. The OF_CORNER_TIME_PCT measures Open Field - Total time in corners under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Cerebellum Gene Expression Correlates for ST_PCT_PPI_70 measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The ST_PCT_PPI_70 measures Prepulse inhibition at 70db 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 ST_PCT_STARTLE_70 measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The ST_PCT_STARTLE_70 measures Acoustic Startle Response Percentage of maximum startle response at 70 db 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
Whole Brain Gene Expression Correlates for COCA_BASE_VEHICLE measured in BXD RI Females & Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The COCA_BASE_VEHICLE measures CPP- Time (s) spent in saline paired compartment a under the domain Cocaine. 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 SPD_TIMEDOWEL0SEC measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The SPD_TIMEDOWEL0SEC measures Dowel Test - Time 0 Sec under the domain Porsolt. 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 URINE measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The URINE measures Novel Open Field Number of urinations 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 URINE measured in BXD RI Females obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The URINE measures Novel Open Field Number of urinations 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
Heterozygote mice from a hybrid cross of C57BL/6J and FVB/NJ had heightened EtOH consumption, preference or blood EtOH concentration compared to either homozygous groups. The magnitude of dominant deviation on Chr. 11, as noted in Fig. 9, was measured after a drinking in the dark paradigm, 24hr two-bottle-choice and subsequent blood ethanol concentration measurement.
Authors:
Phillips TJ, Reed C, Burkhart-Kasch S, Li N, Hitzemann R, Yu CH, Brown LL, Helms ML, Crabbe JC, Belknap JK
cocaine related behavior 12 (Cocrb12) spans 85.558736 - 135.558736 Mbp (NCBI Build 37) on Chr 11. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
QTL for alcohol preference locus on Chr11 at D11Mit35 (80.34 Mbp , Build 37)
Description:
alcohol preference locus spans 55.34 - 105.34 Mbp (NCBI Build 37) on Chr11. 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 Chr11 at D11Mit39 (81.17 Mbp , Build 37)
Description:
nicotine sensitivity spans 56.17 - 106.17 Mbp (NCBI Build 37) on Chr11. 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 Chr11 at D11Mit35 (106.61 Mbp , Build 37)
Description:
alcohol preference locus spans 81.61 - 131.61 Mbp (NCBI Build 37) on Chr11. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
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