Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "alphav-beta3 integrin-IGF-1-IGF1R complex", which is defined as "A protein complex that consists of an alphav-beta3 integrin complex bound to insulin-like growth factor-1 (IGF-1) and type I insulin-like growth factor receptor (IGF1R). IGF1R is a heterotetramer that consists of two alpha-subunits and two beta-subunits." 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 consists of an alphav-beta3 integrin complex bound to insulin-like growth factor-1 (IGF-1) and type I insulin-like growth factor receptor (IGF1R). IGF1R is a heterotetramer that consists of two alpha-subunits and two beta-subunits." [GOC:BHF, GOC:ebc, PMID:19578119]
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
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 plasma glucose. 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:
JY Hwang, X Sim, Y Wu, J Liang, Y Tabara, C Hu, K Hara, CH Tam, Q Cai, Q Zhao, S Jee, F Takeuchi, MJ Go, RT Ong, T Ohkubo, YJ Kim, R Zhang, T Yamauchi, WY So, J Long, D Gu, NR Lee, S Kim, T Katsuya, JH Oh, J Liu, S Umemura, YJ Kim, F Jiang, S Maeda, JC Chan, W Lu, JE Hixson, LS Adair, KJ Jung, T Nabika, JB Bae, MH Lee, M Seielstad, TL Young, YY Teo, Y Kita, N Takashima, H Osawa, SH Lee, MH Shin, DH Shin, BY Choi, J Shi, YT Gao, YB Xiang, W Zheng, N Kato, M Yoon, J He, XO Shu, RC Ma, T Kadowaki, W Jia, T Miki, L Qi, ES Tai, KL Mohlke, BG Han, YS Cho, BJ Kim
Striatum Gene Expression Correlates for ST_PCT_PPI_70 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) 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
Striatum Gene Expression Correlates for ST_PCT_STARTLE_70 measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) 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
Neocortex Gene Expression Correlates for ZM_ECLOSED measured in BXD RI Females & Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The ZM_ECLOSED measures Zero Maze - total entries in closed quadrants 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
Neocortex Gene Expression Correlates for ZM_EOPEN measured in BXD RI Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The ZM_EOPEN measures Zero Maze - total entries in open quadrants 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 ACTI10_SAL measured in BXD RI Females & Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The ACTI10_SAL measures Distance traveled (cm) during the second five minute bin after saline 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
Whole Brain Gene Expression Correlates for ACTI10_SAL measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The ACTI10_SAL measures Distance traveled (cm) during the second five minute bin after saline 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
Whole Brain Gene Expression Correlates for ACTI20_SAL measured in BXD RI Females & Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The ACTI20_SAL measures Distance traveled (cm) during the fourth five minute bin after saline 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
Whole Brain Gene Expression Correlates for ACTI20_SAL measured in BXD RI Females obtained using INIA Brain mRNA M430 (Jun06) RMA. The ACTI20_SAL measures Distance traveled (cm) during the fourth five minute bin after saline 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
Whole Brain Gene Expression Correlates for HIC_SCORE measured in BXD RI Females obtained using INIA Brain mRNA M430 (Jun06) RMA. The HIC_SCORE measures Handling induced convulsion score under the domain Ethanol HIC. 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 LD_DISTANCE measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LD_DISTANCE measures Light-Dark Box Total distance traveled in light and dark compartments 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 MDMA_ACT_MDA_1 measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The MDMA_ACT_MDA_1 measures Locomotor response of 10 mg/kg MDMA injected on Day 2 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
QTL for ethanol conditioned taste aversion on Chr7 at D7Ncvs57 (73.76 Mbp , Build 37)
Description:
ethanol conditioned taste aversion spans 48.76 - 98.76 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 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 alcohol preference locus on Chr7 at D7Mit19 (85.32 Mbp , Build 37)
Description:
alcohol preference locus spans 60.32 - 110.32 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
None - Basal gene expression profiles between C57BL/6J, DBA/2J, 129P3/J, and SWR/J strains DNA microarray Change in gene expression Two-way analysis of variance (ANOVA). 3,457 probe sets (corresponded to 2,870 different transcripts) with significant inter-strain differences (differ by at least 1.2-fold) - False discovery rate [FDR] < 1%, , rank > 3. Such a large disparity in the mouse striatal transcriptome was estimated by comparing nine array replicates prepared per strain from all of the treatment groups. More than half of the identified probe sets exhibited markedly significant results (1,735 with rank > 7). (NIF Method ID 84.1)
Authors:
Korostynski M, Piechota M, Kaminska D, Solecki W, Przewlocki R
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