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 Immune response to smallpox vaccine (IL-6). The EFO term response to vaccine 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:
IG Ovsyannikova, RB Kennedy, M O'Byrne, RM Jacobson, VS Pankratz, GA Poland
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.
H3K4me3 CHiP Seq data for alcohol dependence. Gene Symbol and p-value (unadjusted). Samples were from twenty-three hippocampi from eight people with a history of alcohol user, seven people with a history of cocaine use, and eight matched control subjects.
H3K4me3 CHiP Seq data for Hippocampus from post-mortem sample of people with a history of cocaine use. Gene Symbol and p-value (unadjusted). Samples were from twenty-three hippocampi from eight people with a history of alcohol use, seven people with a history of cocaine use, and eight matched control subjects.
170 differentially expressed in the nucleus accumbens of Long-Evans rats reared in limited bedding and nesting (LBN) conditions. The effect of LBN on morhpine self-administration was investigated. Bilateral NAc specimens were analyzed for gene expression using RNA-seq. Data available at GEO (accession number GSE160495). Data presented are p-values.
Authors:
Evelyn Ordoñes Sanchez, Charlotte C Bavley, Andre U Deutschmann, Rachel Carpenter, Drew R Peterson, Reza Karbalaei, James Flowers, Charleanne M Rogers, Miranda G Langrehr, Cory S Ardekani, Sydney T Famularo, Angela R Bongiovanni, Melissa C Knouse, Stan B Floresco, Lisa A Briand, Mathieu E Wimmer, Debra A Bangasser
Genes that have regions with differential 5-hydroxymethylcytosine (5hmC) levels in response to cocaine in adult (8-10 week) male C57BL/6J mice. 5hmC levels were measured via 5hmC-seq. Data taken from Supplementary Table 2. Values presented are p-values. Data available at GEO with accession number GSE63749.
Adolescent male Sprague-Dawley rats were either exposed to the synthetic cannabinoid WIN 55,212-2 (WIN) prior to cocaine administration or not. Gene expression was evaluated via RNA-seq. Data available at GEO with accession number GSE134935. Data taken from Supplementary Dataset S2. Values presented are p-adjusted values.
Authors:
Maria Scherma, Johanna S Qvist, Arun Asok, Shao-Shan C Huang, Paolo Masia, Matteo Deidda, Ya B Wei, Rajesh K Soni, Walter Fratta, Paola Fadda, Eric R Kandel, Denise B Kandel, Philippe A Melas
Adolescent male Sprague-Dawley rats were either exposed to the synthetic cannabinoid WIN 55,212-2 (WIN) prior to cocaine administration or not. Skipped exon (SE) events were evaluated. Gene expression was evaluated via RNA-seq. Data available at GEO with accession number GSE134935. Data taken from Supplementary Dataset S3. Values presented are p-values.
Authors:
Maria Scherma, Johanna S Qvist, Arun Asok, Shao-Shan C Huang, Paolo Masia, Matteo Deidda, Ya B Wei, Rajesh K Soni, Walter Fratta, Paola Fadda, Eric R Kandel, Denise B Kandel, Philippe A Melas
Adolescent male Sprague-Dawley rats were either exposed to the synthetic cannabinoid WIN 55,212-2 (WIN) prior to cocaine administration or not. Skipped exon (SE) events were evaluated. Gene expression was evaluated via RNA-seq. Data available at GEO with accession number GSE134935. Data taken from Supplementary Dataset S3. Values presented are p-values.
Authors:
Maria Scherma, Johanna S Qvist, Arun Asok, Shao-Shan C Huang, Paolo Masia, Matteo Deidda, Ya B Wei, Rajesh K Soni, Walter Fratta, Paola Fadda, Eric R Kandel, Denise B Kandel, Philippe A Melas
Adolescent male Sprague-Dawley rats were either exposed to the synthetic cannabinoid WIN 55,212-2 (WIN) prior to cocaine administration or not. Skipped exon (SE) events were evaluated. Gene expression was evaluated via RNA-seq. Data available at GEO with accession number GSE134935. Data taken from Supplementary Dataset S3. Values presented are p-values.
Authors:
Maria Scherma, Johanna S Qvist, Arun Asok, Shao-Shan C Huang, Paolo Masia, Matteo Deidda, Ya B Wei, Rajesh K Soni, Walter Fratta, Paola Fadda, Eric R Kandel, Denise B Kandel, Philippe A Melas
Adolescent male Sprague-Dawley rats were either exposed to the synthetic cannabinoid WIN 55,212-2 (WIN) prior to cocaine administration or not. Skipped exon (SE) events were evaluated. Gene expression was evaluated via RNA-seq. Data available at GEO with accession number GSE134935. Data taken from Supplementary Dataset S3. Values presented are p-values.
Authors:
Maria Scherma, Johanna S Qvist, Arun Asok, Shao-Shan C Huang, Paolo Masia, Matteo Deidda, Ya B Wei, Rajesh K Soni, Walter Fratta, Paola Fadda, Eric R Kandel, Denise B Kandel, Philippe A Melas
Adolescent male Sprague-Dawley rats were either exposed to the synthetic cannabinoid WIN 55,212-2 (WIN) prior to cocaine administration or not (+/- WIN and +/- cocaine). Differential synaptosome protein expression was evaluated across all four adolescent treatment groups. Gene expression was evaluated via RNA-seq. Data available at GEO with accession number GSE134935. Data taken from Supplementary Dataset S7. Values presented are p-adjusted values.
Authors:
Maria Scherma, Johanna S Qvist, Arun Asok, Shao-Shan C Huang, Paolo Masia, Matteo Deidda, Ya B Wei, Rajesh K Soni, Walter Fratta, Paola Fadda, Eric R Kandel, Denise B Kandel, Philippe A Melas
Differentially expressed genes in male Sprague-Dawley rats (300-375 g or 250-300 g) following cocaine administration. Some animals expressed the H3.3 Q5A vector, which led to down-regulation of histone H3 glutamine 5 dopaminylation (H3Q5dop), which is involved in midbrain plasticity in response to cocaine. Gene expression was evaluated via RNA-seq. Data taken from Supplemental Table S4 (associated with Fig 2. E, G, and I). Values presented are p-values. Data available at GEO with accession number GSE124055.
Authors:
Ashley E Lepack, Craig T Werner, Andrew F Stewart, Sasha L Fulton, Ping Zhong, Lorna A Farrelly, Alexander C W Smith, Aarthi Ramakrishnan, Yang Lyu, Ryan M Bastle, Jennifer A Martin, Swarup Mitra, Richard M O'Connor, Zi-Jun Wang, Henrik Molina, Gustavo Turecki, Li Shen, Zhen Yan, Erin S Calipari, David M Dietz, Paul J Kenny, Ian Maze
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
Differentially expressed geens in the central amygdala (CeA) of male Sprague-Dawley rats (300-350 g prior to surgery, 325-375 g at start of self-administration) on day 2 following methamphetamine withdrawal. Gene Expression was evaluated via RNA-seq. Data taken from Supplementary Table S2. Values presented are adjusted p-values. Data available from GEO with accession number GSE111243."
Authors:
Hannah M Cates, Xuan Li, Immanuel Purushothaman, Pamela J Kennedy, Li Shen, Yavin Shaham, Eric J Nestler
Differentially expressed geens in the central amygdala (CeA) of male Sprague-Dawley rats (300-350 g prior to surgery, 325-375 g at start of self-administration) on day 35 following methamphetamine withdrawal. Gene Expression was evaluated via RNA-seq. Data taken from Supplementary Table S2. Values presented are adjusted p-values. Data available from GEO with accession number GSE111243."
Authors:
Hannah M Cates, Xuan Li, Immanuel Purushothaman, Pamela J Kennedy, Li Shen, Yavin Shaham, Eric J Nestler
Neocortex Gene Expression Correlates for LM_CUE_ACTIVITY measured in BXD RI Females obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The LM_CUE_ACTIVITY measures Activity in altered context during presentation of cue 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 LM_CUE_SUPPRESS measured in BXD RI Females obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The LM_CUE_SUPPRESS measures Suppression of activity in altered context 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
Hippocampus Gene Expression Correlates for OF_CENTER_DIST_PCT measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The OF_CENTER_DIST_PCT measures Open Field - Percentage of total distance traveled in center 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 ADRE_LEFT_WT measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The ADRE_LEFT_WT measures Left adrenal weight under the domain Adrenals. 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 ADRE_RIGHT_WT measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The ADRE_RIGHT_WT measures Right adrenal weight under the domain Adrenals. 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 OF_TOT_PERIM_DIST_PCT measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The OF_TOT_PERIM_DIST_PCT measures Open Field -Total distance in the perimeter 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
A list of genes whose transcript abundance in the PFC changed significantly 4 hours after an acute dose of ethanol (1.8 g/kg). This list was generated using Fisher's Combined Probability test to analyze saline vs ethanol S-scores across B6 and D2 inbred strains (n=3) and 27 BXD RI lines (n=1). Statistical significance was determined using 1,000 permutations of S-score data and selecting for probe-sets with q-values < 0.05. Aaron Wolen 5-26-10.
Authors:
Wolen AR, Phillips CA, Langston MA, Putman AH, Vorster PJ, Bruce NA, York TP, Williams RW, Miles MF
Renthal W, Kumar A, Xiao G, Wilkinson M, Covington HE 3rd, Maze I, Sikder D, Robison AJ, LaPlant Q, Dietz DM, Russo SJ, Vialou V, Chakravarty S, Kodadek TJ, Stack A, Kabbaj M, Nestler EJ
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