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 Menarche (age at onset). The EFO term age at menarche 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:
EW Demerath, CT Liu, N Franceschini, G Chen, JR Palmer, EN Smith, CT Chen, CB Ambrosone, AM Arnold, EV Bandera, GS Berenson, L Bernstein, A Britton, AR Cappola, CS Carlson, SJ Chanock, W Chen, Z Chen, SL Deming, CE Elks, MK Evans, Z Gajdos, BE Henderson, JJ Hu, S Ingles, EM John, KF Kerr, LN Kolonel, L Le Marchand, X Lu, RC Millikan, SK Musani, NL Nock, K North, S Nyante, MF Press, JL Rodriquez-Gil, EA Ruiz-Narvaez, NJ Schork, SR Srinivasan, NF Woods, W Zheng, RG Ziegler, A Zonderman, G Heiss, B Gwen Windham, M Wellons, SS Murray, M Nalls, T Pastinen, A Rajkovic, J Hirschhorn, L Adrienne Cupples, C Kooperberg, JM Murabito, CA Haiman
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 Gamma gluatamyl transferase levels. The EFO term serum gamma-glutamyl transferase 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:
RP Middelberg, B Benyamin, MH de Moor, NM Warrington, S Gordon, AK Henders, SE Medland, DR Nyholt, EJ de Geus, JJ Hottenga, G Willemsen, LJ Beilin, TA Mori, MJ Wright, AC Heath, PA Madden, DI Boomsma, CE Pennell, GW Montgomery, NG Martin, JB Whitfield
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 Liver enzyme levels (gamma-glutamyl transferase). The EFO term serum gamma-glutamyl transferase 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:
JC Chambers, W Zhang, J Sehmi, X Li, MN Wass, P Van der Harst, H Holm, S Sanna, M Kavousi, SE Baumeister, LJ Coin, G Deng, C Gieger, NL Heard-Costa, JJ Hottenga, B Kühnel, V Kumar, V Lagou, L Liang, J Luan, PM Vidal, I Mateo Leach, PF O'Reilly, JF Peden, N Rahmioglu, P Soininen, EK Speliotes, X Yuan, G Thorleifsson, BZ Alizadeh, LD Atwood, IB Borecki, MJ Brown, P Charoen, F Cucca, D Das, EJ de Geus, AL Dixon, A Döring, G Ehret, GI Eyjolfsson, M Farrall, NG Forouhi, N Friedrich, W Goessling, DF Gudbjartsson, TB Harris, AL Hartikainen, S Heath, GM Hirschfield, A Hofman, G Homuth, E Hyppönen, HL Janssen, T Johnson, AJ Kangas, IP Kema, JP Kühn, S Lai, M Lathrop, MM Lerch, Y Li, TJ Liang, JP Lin, RJ Loos, NG Martin, MF Moffatt, GW Montgomery, PB Munroe, K Musunuru, Y Nakamura, CJ O'Donnell, I Olafsson, BW Penninx, A Pouta, BP Prins, I Prokopenko, R Puls, A Ruokonen, MJ Savolainen, D Schlessinger, JN Schouten, U Seedorf, S Sen-Chowdhry, KA Siminovitch, JH Smit, TD Spector, W Tan, TM Teslovich, T Tukiainen, AG Uitterlinden, MM Van der Klauw, RS Vasan, C Wallace, H Wallaschofski, HE Wichmann, G Willemsen, P Würtz, C Xu, LM Yerges-Armstrong, GR Abecasis, KR Ahmadi, DI Boomsma, M Caulfield, WO Cookson, CM van Duijn, P Froguel, K Matsuda, MI McCarthy, C Meisinger, V Mooser, KH Pietiläinen, G Schumann, H Snieder, MJ Sternberg, RP Stolk, HC Thomas, U Thorsteinsdottir, M Uda, G Waeber, NJ Wareham, DM Waterworth, H Watkins, JB Whitfield, JC Witteman, BH Wolffenbuttel, CS Fox, M Ala-Korpela, K Stefansson, P Vollenweider, H Völzke, EE Schadt, J Scott, MR Järvelin, P Elliott, JS Kooner
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
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 C-reactive protein levels. The EFO term C-reactive protein 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 Dehghan, J Dupuis, M Barbalic, JC Bis, G Eiriksdottir, C Lu, N Pellikka, H Wallaschofski, J Kettunen, P Henneman, J Baumert, DP Strachan, C Fuchsberger, V Vitart, JF Wilson, G Paré, S Naitza, ME Rudock, I Surakka, EJ de Geus, BZ Alizadeh, J Guralnik, A Shuldiner, T Tanaka, RY Zee, RB Schnabel, V Nambi, M Kavousi, S Ripatti, M Nauck, NL Smith, AV Smith, J Sundvall, P Scheet, Y Liu, A Ruokonen, LM Rose, MG Larson, RC Hoogeveen, NB Freimer, A Teumer, RP Tracy, LJ Launer, JE Buring, JF Yamamoto, AR Folsom, EJ Sijbrands, J Pankow, P Elliott, JF Keaney, W Sun, AP Sarin, JD Fontes, S Badola, BC Astor, A Hofman, A Pouta, K Werdan, KH Greiser, O Kuss, HE Meyer zu Schwabedissen, J Thiery, Y Jamshidi, IM Nolte, N Soranzo, TD Spector, H Völzke, AN Parker, T Aspelund, D Bates, L Young, K Tsui, DS Siscovick, X Guo, JI Rotter, M Uda, D Schlessinger, I Rudan, AA Hicks, BW Penninx, B Thorand, C Gieger, J Coresh, G Willemsen, TB Harris, AG Uitterlinden, MR Järvelin, K Rice, D Radke, V Salomaa, K Willems van Dijk, E Boerwinkle, RS Vasan, L Ferrucci, QD Gibson, S Bandinelli, H Snieder, DI Boomsma, X Xiao, H Campbell, C Hayward, PP Pramstaller, CM van Duijn, L Peltonen, BM Psaty, V Gudnason, PM Ridker, G Homuth, W Koenig, CM Ballantyne, JC Witteman, EJ Benjamin, M Perola, DI Chasman
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 Menarche (age at onset). The EFO term age at menarche 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:
CE Elks, JR Perry, P Sulem, DI Chasman, N Franceschini, C He, KL Lunetta, JA Visser, EM Byrne, DL Cousminer, DF Gudbjartsson, T Esko, B Feenstra, JJ Hottenga, DL Koller, Z Kutalik, P Lin, M Mangino, M Marongiu, PF McArdle, AV Smith, L Stolk, SH van Wingerden, JH Zhao, E Albrecht, T Corre, E Ingelsson, C Hayward, PK Magnusson, EN Smith, S Ulivi, NM Warrington, L Zgaga, H Alavere, N Amin, T Aspelund, S Bandinelli, I Barroso, GS Berenson, S Bergmann, H Blackburn, E Boerwinkle, JE Buring, F Busonero, H Campbell, SJ Chanock, W Chen, MC Cornelis, D Couper, AD Coviello, P d'Adamo, U de Faire, EJ de Geus, P Deloukas, A Döring, GD Smith, DF Easton, G Eiriksdottir, V Emilsson, J Eriksson, L Ferrucci, AR Folsom, T Foroud, M Garcia, P Gasparini, F Geller, C Gieger, V Gudnason, P Hall, SE Hankinson, L Ferreli, AC Heath, DG Hernandez, A Hofman, FB Hu, T Illig, MR Järvelin, AD Johnson, D Karasik, KT Khaw, DP Kiel, TO Kilpeläinen, I Kolcic, P Kraft, LJ Launer, JS Laven, S Li, J Liu, D Levy, NG Martin, WL McArdle, M Melbye, V Mooser, JC Murray, SS Murray, MA Nalls, P Navarro, M Nelis, AR Ness, K Northstone, BA Oostra, M Peacock, LJ Palmer, A Palotie, G Paré, AN Parker, NL Pedersen, L Peltonen, CE Pennell, P Pharoah, O Polasek, AS Plump, A Pouta, E Porcu, T Rafnar, JP Rice, SM Ring, F Rivadeneira, I Rudan, C Sala, V Salomaa, S Sanna, D Schlessinger, NJ Schork, A Scuteri, AV Segrè, AR Shuldiner, N Soranzo, U Sovio, SR Srinivasan, DP Strachan, ML Tammesoo, E Tikkanen, D Toniolo, K Tsui, L Tryggvadottir, J Tyrer, M Uda, RM van Dam, JB van Meurs, P Vollenweider, G Waeber, NJ Wareham, DM Waterworth, MN Weedon, HE Wichmann, G Willemsen, JF Wilson, AF Wright, L Young, G Zhai, WV Zhuang, LJ Bierut, DI Boomsma, HA Boyd, L Crisponi, EW Demerath, CM van Duijn, MJ Econs, TB Harris, DJ Hunter, RJ Loos, A Metspalu, GW Montgomery, PM Ridker, TD Spector, EA Streeten, K Stefansson, U Thorsteinsdottir, AG Uitterlinden, E Widen, JM Murabito, KK Ong, A Murray
GWAS: low density lipoprotein cholesterol measurement, C-reactive protein measurement
Description:
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 C-reactive protein levels or LDL-cholesterol levels (pleiotropy). The EFO term low density lipoprotein cholesterol measurement, C-reactive protein 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:
S Ligthart, A Vaez, YH Hsu, R Stolk, AG Uitterlinden, A Hofman, BZ Alizadeh, OH Franco, A Dehghan
GWAS: total cholesterol measurement, C-reactive protein measurement
Description:
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 C-reactive protein levels or total cholesterol levels (pleiotropy). The EFO term total cholesterol measurement, C-reactive protein 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:
S Ligthart, A Vaez, YH Hsu, R Stolk, AG Uitterlinden, A Hofman, BZ Alizadeh, OH Franco, A Dehghan
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 Menarche (age at onset). The EFO term age at menarche 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:
JR Perry, F Day, CE Elks, P Sulem, DJ Thompson, T Ferreira, C He, DI Chasman, T Esko, G Thorleifsson, E Albrecht, WQ Ang, T Corre, DL Cousminer, B Feenstra, N Franceschini, A Ganna, AD Johnson, S Kjellqvist, KL Lunetta, G McMahon, IM Nolte, L Paternoster, E Porcu, AV Smith, L Stolk, A Teumer, N Tšernikova, E Tikkanen, S Ulivi, EK Wagner, N Amin, LJ Bierut, EM Byrne, JJ Hottenga, DL Koller, M Mangino, TH Pers, LM Yerges-Armstrong, J Hua Zhao, IL Andrulis, H Anton-Culver, F Atsma, S Bandinelli, MW Beckmann, J Benitez, C Blomqvist, SE Bojesen, MK Bolla, B Bonanni, H Brauch, H Brenner, JE Buring, J Chang-Claude, S Chanock, J Chen, G Chenevix-Trench, JM Collée, FJ Couch, D Couper, AD Coviello, A Cox, K Czene, AP D'adamo, G Davey Smith, I De Vivo, EW Demerath, J Dennis, P Devilee, AK Dieffenbach, AM Dunning, G Eiriksdottir, JG Eriksson, PA Fasching, L Ferrucci, D Flesch-Janys, H Flyger, T Foroud, L Franke, ME Garcia, M García-Closas, F Geller, EE de Geus, GG Giles, DF Gudbjartsson, V Gudnason, P Guénel, S Guo, P Hall, U Hamann, R Haring, CA Hartman, AC Heath, A Hofman, MJ Hooning, JL Hopper, FB Hu, DJ Hunter, D Karasik, DP Kiel, JA Knight, VM Kosma, Z Kutalik, S Lai, D Lambrechts, A Lindblom, R Mägi, PK Magnusson, A Mannermaa, NG Martin, G Masson, PF McArdle, WL McArdle, M Melbye, K Michailidou, E Mihailov, L Milani, RL Milne, H Nevanlinna, P Neven, EA Nohr, AJ Oldehinkel, BA Oostra, A Palotie, M Peacock, NL Pedersen, P Peterlongo, J Peto, PD Pharoah, DS Postma, A Pouta, K Pylkäs, P Radice, S Ring, F Rivadeneira, A Robino, LM Rose, A Rudolph, V Salomaa, S Sanna, D Schlessinger, MK Schmidt, MC Southey, U Sovio, MJ Stampfer, D Stöckl, AM Storniolo, NJ Timpson, J Tyrer, JA Visser, P Vollenweider, H Völzke, G Waeber, M Waldenberger, H Wallaschofski, Q Wang, G Willemsen, R Winqvist, BH Wolffenbuttel, MJ Wright, DI Boomsma, MJ Econs, KT Khaw, RJ Loos, MI McCarthy, GW Montgomery, JP Rice, EA Streeten, U Thorsteinsdottir, CM van Duijn, BZ Alizadeh, S Bergmann, E Boerwinkle, HA Boyd, L Crisponi, P Gasparini, C Gieger, TB Harris, E Ingelsson, MR Järvelin, P Kraft, D Lawlor, A Metspalu, CE Pennell, PM Ridker, H Snieder, TI Sørensen, TD Spector, DP Strachan, AG Uitterlinden, NJ Wareham, E Widen, M Zygmunt, A Murray, DF Easton, K Stefansson, JM Murabito, KK Ong
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 Total ventricular volume (Alzheimer's disease interaction). The EFO term Alzheimers disease, brain volume 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:
SJ Furney, A Simmons, G Breen, I Pedroso, K Lunnon, P Proitsi, A Hodges, J Powell, LO Wahlund, I Kloszewska, P Mecocci, H Soininen, M Tsolaki, B Vellas, C Spenger, M Lathrop, L Shen, S Kim, AJ Saykin, MW Weiner, S Lovestone
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 genes from Neovascular AMD compared to Normal RPE
Description:
Transcriptome profiling from macular retina and RPE/choroid samples from 27 unrelated eye tissue donors, was performed using RNA-sequencing. Human donor eye collection were obtained from Utah Lions Eye Bank within a 6-hour post-mortem interval and donors aged 60-90 years. Sample types were Normal Retina, Intermediate AMD Retina, Neovascular AMD Retina, Normal macular retina pigment epithelium (RPE), Intermediate AMD RPE, and Neovascular AMD RPE. Age Related Macular Degeneration (AMD) phenotyping was determined using the Age-Related Eye Disease Study (AREDS) severity grading scale, where AREDS category 0/1 was considered normal, AREDS category 3 intermediate AMD, and AREDS category 4b neovascular AMD. Samples from Neovascular AMD (AREDS3) macular retina pigment epithelium (RPE) compared to Normal RPE, and are presented with fold change > 1.5 and and P < 0.05. This gene set was annotated from the Supplementry Table of BioRxiv pre-print paper ‘Patterns of gene expression and allele-specific expression vary among macular tissues and clinical stages of Age-related Macular Degeneration’ by Zhang et.al (2022) doi: https://doi.org/10.1101/2022.12.19.521092
Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder. Transcriptomic profile of 20 control subjects and 20 OUD subjects in brain region DLPFC and NAC. Analyzed using GEO2R (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174409) separately for each brain region, comparing OUD and control samples.
Authors:
Xiangning Xue, Wei Zong, Jill R Glausier, Sam-Moon Kim, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Marianne L Seney, Ryan W Logan
Postmortem tissue samples of the dorsolateral prefrontal cortex (DLPFC) from 153 deceased individuals (Mage = 35.4; 62% male; 77% European ancestry). Study groups included 72 brain samples from individuals who died of acute opioid intoxication, 53 psychiatric controls, and 28 normal controls. Whole transcriptome RNA-sequencing was used to generate exon counts, and differential expression was tested using limma-voom. Analyses were adjusted for relevant sociodemographic characteristics, technical covariates, and cryptic relatedness using quality surrogate variables. Weighted correlation network analysis and gene set enrichment analyses also were conducted.
Authors:
David W Sosnowski, Andrew E Jaffe, Ran Tao, Amy Deep-Soboslay, Chang Shu, Sarven Sabunciyan, Joel E Kleinman, Thomas M Hyde, Brion S Maher
Changes in gene expression in neuron-like, SH-SY5Y human neuroblastoma cells, is analyzed following 24 hours of continuous exposure to 1 mM nicotine and several nicotine-induced cellular changes in acetylcholine receptor are found. Microarray analysis of gene expression shows significantly and consistently altered genes during nicotine treatment with a p-value of less than 0.01.
Authors:
Konu O, Kane JK, Barrett T, Vawter MP, Chang R, Ma JZ, Donovan DM, Sharp B, Becker KG, Li MD
Whole Brain Gene Expression Correlates for ENTRIES_CLOSED measured in BXD RI Females obtained using INIA Brain mRNA M430 (Jun06) RMA. The ENTRIES_CLOSED measures Number of entries into closed arms of plus maze 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
Hippocampus Gene Expression Correlates for ACTI10_SAL measured in BXD RI Females obtained using GeneNetwork Hippocampus Consortium M430v2 (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
Hippocampus Gene Expression Correlates for AMCNT165 measured in BXD RI Females obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The AMCNT165 measures Morphine photocell counts minutes 150-165 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
GeneWeaver