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 Colorectal cancer. The EFO term colorectal cancer 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:
WH Jia, B Zhang, K Matsuo, A Shin, YB Xiang, SH Jee, DH Kim, Z Ren, Q Cai, J Long, J Shi, W Wen, G Yang, RJ Delahanty, BT Ji, ZZ Pan, F Matsuda, YT Gao, JH Oh, YO Ahn, EJ Park, HL Li, JW Park, J Jo, JY Jeong, S Hosono, G Casey, U Peters, XO Shu, YX Zeng, W Zheng
Transcriptomic study of mouse embryonic neural stem cell differentiation under ethanol treatment.Top 50 up and top 50 down regulated genes from microarray analysis. Fold change uploaded. Study identified 496 differentially expressed, author contacted for full list.
Authors:
Mandal C, Park JH, Choi MR, Kim SH, Badejo AC, Chai JC, Lee YS, Jung KH, Chai YG
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 Red blood cell traits. The EFO term mean corpuscular hemoglobin 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:
P van der Harst, W Zhang, I Mateo Leach, A Rendon, N Verweij, J Sehmi, DS Paul, U Elling, H Allayee, X Li, A Radhakrishnan, ST Tan, K Voss, CX Weichenberger, CA Albers, A Al-Hussani, FW Asselbergs, M Ciullo, F Danjou, C Dina, T Esko, DM Evans, L Franke, M Gögele, J Hartiala, M Hersch, H Holm, JJ Hottenga, S Kanoni, ME Kleber, V Lagou, C Langenberg, LM Lopez, LP Lyytikäinen, O Melander, F Murgia, IM Nolte, PF O'Reilly, S Padmanabhan, A Parsa, N Pirastu, E Porcu, L Portas, I Prokopenko, JS Ried, SY Shin, CS Tang, A Teumer, M Traglia, S Ulivi, HJ Westra, J Yang, JH Zhao, F Anni, A Abdellaoui, A Attwood, B Balkau, S Bandinelli, F Bastardot, B Benyamin, BO Boehm, WO Cookson, D Das, PI de Bakker, RA de Boer, EJ de Geus, MH de Moor, M Dimitriou, FS Domingues, A Döring, G Engström, GI Eyjolfsson, L Ferrucci, K Fischer, R Galanello, SF Garner, B Genser, QD Gibson, G Girotto, DF Gudbjartsson, SE Harris, AL Hartikainen, CE Hastie, B Hedblad, T Illig, J Jolley, M Kähönen, IP Kema, JP Kemp, L Liang, H Lloyd-Jones, RJ Loos, S Meacham, SE Medland, C Meisinger, Y Memari, E Mihailov, K Miller, MF Moffatt, M Nauck, M Novatchkova, T Nutile, I Olafsson, PT Onundarson, D Parracciani, BW Penninx, L Perseu, A Piga, G Pistis, A Pouta, U Puc, O Raitakari, SM Ring, A Robino, D Ruggiero, A Ruokonen, A Saint-Pierre, C Sala, A Salumets, J Sambrook, H Schepers, CO Schmidt, HH Silljé, R Sladek, JH Smit, JM Starr, J Stephens, P Sulem, T Tanaka, U Thorsteinsdottir, V Tragante, WH van Gilst, LJ van Pelt, DJ van Veldhuisen, U Völker, JB Whitfield, G Willemsen, BR Winkelmann, G Wirnsberger, A Algra, F Cucca, AP d'Adamo, J Danesh, IJ Deary, AF Dominiczak, P Elliott, P Fortina, P Froguel, P Gasparini, A Greinacher, SL Hazen, MR Jarvelin, KT Khaw, T Lehtimäki, W Maerz, NG Martin, A Metspalu, BD Mitchell, GW Montgomery, C Moore, G Navis, M Pirastu, PP Pramstaller, R Ramirez-Solis, E Schadt, J Scott, AR Shuldiner, GD Smith, JG Smith, H Snieder, R Sorice, TD Spector, K Stefansson, M Stumvoll, WH Tang, D Toniolo, A Tönjes, PM Visscher, P Vollenweider, NJ Wareham, BH Wolffenbuttel, DI Boomsma, JS Beckmann, GV Dedoussis, P Deloukas, MA Ferreira, S Sanna, M Uda, AA Hicks, JM Penninger, C Gieger, JS Kooner, WH Ouwehand, N Soranzo, JC Chambers
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 Colorectal cancer. The EFO term colorectal cancer 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:
B Zhang, WH Jia, K Matsuda, SS Kweon, K Matsuo, YB Xiang, A Shin, SH Jee, DH Kim, Q Cai, J Long, J Shi, W Wen, G Yang, Y Zhang, C Li, B Li, Y Guo, Z Ren, BT Ji, ZZ Pan, A Takahashi, MH Shin, F Matsuda, YT Gao, JH Oh, S Kim, YO Ahn, AT Chan, J Chang-Claude, ML Slattery, SB Gruber, FR Schumacher, SL Stenzel, G Casey, HR Kim, JY Jeong, JW Park, HL Li, S Hosono, SH Cho, M Kubo, XO Shu, YX Zeng, W Zheng
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 Red blood cell count. The EFO term erythrocyte count 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 Kamatani, K Matsuda, Y Okada, M Kubo, N Hosono, Y Daigo, Y Nakamura, N Kamatani
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
Gene expression in 212,713 ventral midbrain single nuclei from 95 individuals with history of opioid misuse, and individuals without drug exposure. Chronic exposure to opioids was not associated with change in proportions of glial and neuronal subtypes, however glial transcriptomes were broadly altered, involving 9.5 - 6.2% of expressed genes within microglia, oligodendrocytes, and astrocytes. Genes associated with activation of the immune response including interferon, NFkB signaling, and cell motility pathways were upregulated, contrasting with down-regulated expression of synaptic signaling and plasticity genes in ventral midbrain non-dopaminergic neurons. Ventral midbrain transcriptomic reprogramming in the context of chronic opioid exposure included 325 genes that previous genome-wide studies had linked to risk of substance use traits in the broader population.
Authors:
Julong Wei, Tova Y Lambert, Aditi Valada, Nikhil Patel, Kellie Walker, Jayna Lenders, Carl J Schmidt, Marina Iskhakova, Adnan Alazizi, Henriette Mair-Meijers, Deborah C Mash, Francesca Luca, Roger Pique-Regi, Michael J Bannon, Schahram Akbarian
Opioid use disorder_human_dorsolateral prefrontal cortex_coefficient
Description:
RNA sequencing on the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc) from unaffected comparison subjects (n = 20) and subjects diagnosed with opioid use disorder OUD (n = 20). Transcriptomic analyses identified differentially expressed transcripts and investigated the transcriptional coherence between brain regions using rank-rank hypergeometric orderlap.transcriptional differences by brain region in unaffected comparison subjects, finding unique transcriptional profiles in the DLPFC and NAc
Authors:
Marianne L Seney, Sam-Moon Kim, Jill R Glausier, Mariah A Hildebrand, Xiangning Xue, Wei Zong, Jiebiao Wang, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Zachary Freyberg, Ryan W Logan
Opioid use disorder_human_nucleus accumbens_coefficient
Description:
RNA sequencing on the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc) from unaffected comparison subjects (n = 20) and subjects diagnosed with opioid use disorder OUD (n = 20). Transcriptomic analyses identified differentially expressed transcripts and investigated the transcriptional coherence between brain regions using rank-rank hypergeometric orderlap.transcriptional differences by brain region in unaffected comparison subjects, finding unique transcriptional profiles in the DLPFC and NAc
Authors:
Marianne L Seney, Sam-Moon Kim, Jill R Glausier, Mariah A Hildebrand, Xiangning Xue, Wei Zong, Jiebiao Wang, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Zachary Freyberg, Ryan W Logan
Examination of changes in gene expression induced by repeated administration of the mGlu5 antagonists MPEP and MTEP. Male Wistar rats (n=5 per treatment group) were administered MPEP (10 mg/kg), MTEP (10 mg/kg) or vehicle intraperitoneally twice daily for 5 days.
Hippocampus Gene Expression Correlates for TAILCLIP_LAT_SEC measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) 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
Hippocampus Gene Expression Correlates for TAILCLIP_LAT_SEC measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) 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 ACTI15_SAL measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The ACTI15_SAL measures Distance traveled (cm) during the third 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
Cerebellum Gene Expression Correlates for C2HCOUNT45 measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The C2HCOUNT45 measures Open Field locomotion (activity beam breaks) 30-45 min post 2nd cocaine 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
Whole Brain Gene Expression Correlates for NEPCOUNT30 measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The NEPCOUNT30 measures Novel environment locomotion (activity beam breaks) 15-30 min in the periphery 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
Whole Brain Gene Expression Correlates for NEPCOUNT30 measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The NEPCOUNT30 measures Novel environment locomotion (activity beam breaks) 15-30 min in the periphery under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Whole Brain Gene Expression Correlates for NEPCOUNT30 measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The NEPCOUNT30 measures Novel environment locomotion (activity beam breaks) 15-30 min in the periphery under the domain Cocaine. The correlates were thresholded at a p-value of less than 0.001.
Whole Brain Gene Expression Correlates for NEPDIST30 measured in BXD RI Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The NEPDIST30 measures Novel environment distance (cm) travelled min 15-30 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
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