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 Subcortical brain region volumes. The EFO term putamen volume 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:
DP Hibar, JL Stein, ME Renteria, A Arias-Vasquez, S Desrivières, N Jahanshad, R Toro, K Wittfeld, L Abramovic, M Andersson, BS Aribisala, NJ Armstrong, M Bernard, MM Bohlken, MP Boks, J Bralten, AA Brown, MM Chakravarty, Q Chen, CR Ching, G Cuellar-Partida, A den Braber, S Giddaluru, AL Goldman, O Grimm, T Guadalupe, J Hass, G Woldehawariat, AJ Holmes, M Hoogman, D Janowitz, T Jia, S Kim, M Klein, B Kraemer, PH Lee, LM Olde Loohuis, M Luciano, C Macare, KA Mather, M Mattheisen, Y Milaneschi, K Nho, M Papmeyer, A Ramasamy, SL Risacher, R Roiz-Santiañez, EJ Rose, A Salami, PG Sämann, L Schmaal, AJ Schork, J Shin, LT Strike, A Teumer, MM van Donkelaar, KR van Eijk, RK Walters, LT Westlye, CD Whelan, AM Winkler, MP Zwiers, S Alhusaini, L Athanasiu, S Ehrlich, MM Hakobjan, CB Hartberg, UK Haukvik, AJ Heister, D Hoehn, D Kasperaviciute, DC Liewald, LM Lopez, RR Makkinje, M Matarin, MA Naber, DR McKay, M Needham, AC Nugent, B Pütz, NA Royle, L Shen, E Sprooten, D Trabzuni, SS van der Marel, KJ van Hulzen, E Walton, C Wolf, L Almasy, D Ames, S Arepalli, AA Assareh, ME Bastin, H Brodaty, KB Bulayeva, MA Carless, S Cichon, A Corvin, JE Curran, M Czisch, GI de Zubicaray, A Dillman, R Duggirala, TD Dyer, S Erk, IO Fedko, L Ferrucci, TM Foroud, PT Fox, M Fukunaga, JR Gibbs, HH Göring, RC Green, S Guelfi, NK Hansell, CA Hartman, K Hegenscheid, A Heinz, DG Hernandez, DJ Heslenfeld, PJ Hoekstra, F Holsboer, G Homuth, JJ Hottenga, M Ikeda, CR Jack, M Jenkinson, R Johnson, R Kanai, M Keil, JW Kent, P Kochunov, JB Kwok, SM Lawrie, X Liu, DL Longo, KL McMahon, E Meisenzahl, I Melle, S Mohnke, GW Montgomery, JC Mostert, TW Mühleisen, MA Nalls, TE Nichols, LG Nilsson, MM Nöthen, K Ohi, RL Olvera, R Perez-Iglesias, GB Pike, SG Potkin, I Reinvang, S Reppermund, M Rietschel, N Romanczuk-Seiferth, GD Rosen, D Rujescu, K Schnell, PR Schofield, C Smith, VM Steen, JE Sussmann, A Thalamuthu, AW Toga, BJ Traynor, J Troncoso, JA Turner, MC Valdés Hernández, D van 't Ent, M van der Brug, NJ van der Wee, MJ van Tol, DJ Veltman, TH Wassink, E Westman, RH Zielke, AB Zonderman, DG Ashbrook, R Hager, L Lu, FJ McMahon, DW Morris, RW Williams, HG Brunner, RL Buckner, JK Buitelaar, W Cahn, VD Calhoun, GL Cavalleri, B Crespo-Facorro, AM Dale, GE Davies, N Delanty, C Depondt, S Djurovic, WC Drevets, T Espeseth, RL Gollub, BC Ho, W Hoffmann, N Hosten, RS Kahn, S Le Hellard, A Meyer-Lindenberg, B Müller-Myhsok, M Nauck, L Nyberg, M Pandolfo, BW Penninx, JL Roffman, SM Sisodiya, JW Smoller, H van Bokhoven, NE van Haren, H Völzke, H Walter, MW Weiner, W Wen, T White, I Agartz, OA Andreassen, J Blangero, DI Boomsma, RM Brouwer, DM Cannon, MR Cookson, EJ de Geus, IJ Deary, G Donohoe, G Fernández, SE Fisher, C Francks, DC Glahn, HJ Grabe, O Gruber, J Hardy, R Hashimoto, HE Hulshoff Pol, EG Jönsson, I Kloszewska, S Lovestone, VS Mattay, P Mecocci, C McDonald, AM McIntosh, RA Ophoff, T Paus, Z Pausova, M Ryten, PS Sachdev, AJ Saykin, A Simmons, A Singleton, H Soininen, JM Wardlaw, ME Weale, DR Weinberger, HH Adams, LJ Launer, S Seiler, R Schmidt, G Chauhan, CL Satizabal, JT Becker, L Yanek, SJ van der Lee, M Ebling, B Fischl, WT Longstreth, D Greve, H Schmidt, P Nyquist, LN Vinke, CM van Duijn, L Xue, B Mazoyer, JC Bis, V Gudnason, S Seshadri, MA Ikram, NG Martin, MJ Wright, G Schumann, B Franke, PM Thompson, SE Medland
chr14q22
Genes in cytogenetic band chr14q22
c1 - Positional genesets for each human chromosome and cytogenetic band.
Molecular Signatures Database (MSigDB) Geneset. This geneset was imported from one of the MSigDB collections.
gene2msig v. 0.1.0
Last updated 2015.08.31
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
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
Gene expression changes in the post-mortem nucleus accumbens of chronic heroin abusers. Overall, little overlap in gene expression profiles was seen between the two drug-abusing cohorts: out of the approximately 39,000 transcripts investigated, the abundance of only 25 was significantly changed in both cocaine and heroin abusers, with nearly one-half of these being altered in opposite directions. 1050 Transcripts had different in abundance between the majority of heroin subjects and their matched controls.
Striatum Gene Expression Correlates for ACTI_DIFF_05 measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The ACTI_DIFF_05 measures Difference in distance traveled (cm) during the first five min (saline-ethanol) 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 AMDIST15 measured in BXD RI Females obtained using INIA Brain mRNA M430 (Jun06) RMA. The AMDIST15 measures Morphine distance (cm) travelled minutes 0-15 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
Hippocampus Gene Expression Correlates for C1HCOUNT30 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HCOUNT30 measures Open Field locomotion 15-30 min post 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
Hippocampus Gene Expression Correlates for C2HCOUNT30 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C2HCOUNT30 measures Open Field locomotion (activity beam breaks) 15-30 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
Hippocampus Gene Expression Correlates for C2HDIS30 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C2HDIS30 measures Open Field locomotion (cm) 15-30 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
Hippocampus Gene Expression Correlates for LOC_CHCL_ACOUNT_3 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LOC_CHCL_ACOUNT_3 measures Cocaine TOTAL locomotion (activity beam breaks) 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
Hippocampus Gene Expression Correlates for LOC_CHCL_ADIST_3 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LOC_CHCL_ADIST_3 measures Cocaine TOTAL locomotion ( cm in 1 hr) 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
Hippocampus Gene Expression Correlates for SEN_CHCL_ACOUNT_4 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The SEN_CHCL_ACOUNT_4 measures Cocaine Sensitization - TOTAL locomotion (activity beam breaks) 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
Hippocampus Gene Expression Correlates for SEN_CHCL_ADIST_4 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The SEN_CHCL_ADIST_4 measures Cocaine Sensitization - TOTAL locomotion ( cm in 1 hr) 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
Hippocampus Gene Expression Correlates for C1HCOUNT15 measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HCOUNT15 measures Open Field locomotion 0-15 min post 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
Hippocampus Gene Expression Correlates for C1HCOUNT15 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HCOUNT15 measures Open Field locomotion 0-15 min post 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
Hippocampus Gene Expression Correlates for C1HDIS15 measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HDIS15 measures Open Field locomotion (cm) 0-15 min post 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
Hippocampus Gene Expression Correlates for C1HDIS15 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HDIS15 measures Open Field locomotion (cm) 0-15 min post 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
Hippocampus Gene Expression Correlates for C2HCOUNT15 measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C2HCOUNT15 measures Open Field locomotion (activity beam breaks) 0-15 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
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