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 Mucinous ovarian carcinoma. The EFO term ovarian mucinous adenocarcinoma 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:
LE Kelemen, K Lawrenson, J Tyrer, Q Li, JM Lee, JH Seo, CM Phelan, J Beesley, X Chen, TJ Spindler, KK Aben, H Anton-Culver, N Antonenkova
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 Sleep duration (oversleepers vs undersleepers). The EFO term sleep duration 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:
SE Jones, J Tyrrell, AR Wood, RN Beaumont, KS Ruth, MA Tuke, H Yaghootkar, Y Hu, M Teder-Laving, C Hayward, T Roenneberg, JF Wilson, F Del Greco, AA Hicks, C Shin, CH Yun, SK Lee, A Metspalu, EM Byrne, PR Gehrman, H Tiemeier, KV Allebrandt, RM Freathy, A Murray, DA Hinds, TM Frayling, MN Weedon
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 Sleep duration. The EFO term sleep duration 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:
DJ Gottlieb, K Hek, TH Chen, NF Watson, G Eiriksdottir, EM Byrne, M Cornelis, SC Warby, S Bandinelli, L Cherkas, DS Evans, HJ Grabe, J Lahti, M Li, T Lehtimäki, T Lumley, KD Marciante, L Pérusse, BM Psaty, J Robbins, GJ Tranah, JM Vink, JB Wilk, JM Stafford, C Bellis, R Biffar, C Bouchard, B Cade, GC Curhan, JG Eriksson, R Ewert, L Ferrucci, T Fülöp, PR Gehrman, R Goodloe, TB Harris, AC Heath, D Hernandez, A Hofman, JJ Hottenga, DJ Hunter, MK Jensen, AD Johnson, M Kähönen, L Kao, P Kraft, EK Larkin, DS Lauderdale, AI Luik, M Medici, GW Montgomery, A Palotie, SR Patel, G Pistis, E Porcu, L Quaye, O Raitakari, S Redline, EB Rimm, JI Rotter, AV Smith, TD Spector, A Teumer, AG Uitterlinden, MC Vohl, E Widen, G Willemsen, T Young, X Zhang, Y Liu, J Blangero, DI Boomsma, V Gudnason, F Hu, M Mangino, NG Martin, GT O'Connor, KL Stone, T Tanaka, J Viikari, SA Gharib, NM Punjabi, K Räikkönen, H Völzke, E Mignot, H Tiemeier
The total transcriptome including genes that are differentially expressed in cocaine addicts compared to control subjects. Post-mortem brain samples were collected from the dorsolateral prefrontal cortex (dlPFC) of the cocaine addict group and the control group. To assess gene expression, RNA-seq was performed. Data taken from Supplementary Table 2. Values presented are k.diff values. Data available from GEO with accession number GSE99349."
Authors:
Efrain A Ribeiro, Joseph R Scarpa, Susanna P Garamszegi, Andrew Kasarskis, Deborah C Mash, Eric J Nestler
Data from GEO GSE194368 and analyzed using GEO2R, only top gene shown. Authors identified transcriptional adaptations of GR signaling in the amygdala of humans with OUD. Thus, GRs, their coregulators and downstream systems may represent viable therapeutic targets to treat the “stress side” of OUD.
Authors:
Stephanie A Carmack, Janaina C M Vendruscolo, M Adrienne McGinn, Jorge Miranda-Barrientos, Vez Repunte-Canonigo, Gabriel D Bosse, Daniele Mercatelli, Federico M Giorgi, Yu Fu, Anthony J Hinrich, Francine M Jodelka, Karen Ling, Robert O Messing, Randall T Peterson, Frank Rigo, Scott Edwards, Pietro P Sanna, Marisela Morales, Michelle L Hastings, George F Koob, Leandro F Vendruscolo
Cerebellum Gene Expression Correlates for LM_PAIR3 measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The LM_PAIR3 measures Activity during 3rd tone shock pairing 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 COCA_BASE_DRUG measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The COCA_BASE_DRUG measures CPP - Time (s) in drug-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
Striatum Gene Expression Correlates for COCA_TIME_BASELINE measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The COCA_TIME_BASELINE measures Cocaine CPP - Proportion of time spent in conditioned side prior to conditioning 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
Analyzed the gene expression profile of a homogeneous population of duodenal epithelial cells taken from patients with active celiac disease, in comparison to control patients. Of the 3,800 genes present on the array (all of which have been previously annotated), 3549 had sufficient data across the five experiments for comparison. Many of these genes showed fold-change ratios with little or no deviation from 1. Thus, to focus on only differentially expressed genes, the list was filtered on a fo
Authors:
Bracken S, Byrne G, Kelly J, Jackson J, Feighery C
QTL for ethanol conditioned taste aversion on Chr2 at NA (35.13 Mbp , Build 37)
Description:
ethanol conditioned taste aversion spans 10.13 - 60.13 Mbp (NCBI Build 37) on Chr2. 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 Chr2 at Brp13 (41.42 Mbp , Build 37)
Description:
METH responses for climbing spans 16.42 - 66.42 Mbp (NCBI Build 37) on Chr2. 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 ethanol consumption on Chr2 at D2Mit7 (47.24 Mbp , Build 37)
Description:
ethanol consumption spans 22.24 - 72.24 Mbp (NCBI Build 37) on Chr2. 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 'resveratrol' (C059514). Incorporates data from 16 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Papio that interact with the MeSH term 'Cocaine' (D003042). 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 'Tretinoin' (D014212). Incorporates data from 1 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Bos taurus that interact with the MeSH term 'Colforsin' (D005576). Incorporates data from 1 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 'Aflatoxin B1' (D016604). 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 '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.
Genes associated with Homo sapiens that interact with the MeSH term 'butyraldehyde' (C018475). 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 'decitabine' (C014347). Incorporates data from 2 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 '2-amino-4-phenylbutyric acid' (C014328). Incorporates data from 1822 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
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