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 Early response to risperidone in schizophrenia. The EFO term response to risperidone 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:
E Sacchetti, C Magri, A Minelli, P Valsecchi, M Traversa, S Calza, A Vita, M Gennarelli
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 Major depressive disorder (broad). The EFO term unipolar depression 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:
SI Shyn, J Shi, JB Kraft, JB Potash, JA Knowles, MM Weissman, HA Garriock, JS Yokoyama, PJ McGrath, EJ Peters, WA Scheftner, W Coryell, WB Lawson, D Jancic, PV Gejman, AR Sanders, P Holmans, SL Slager, DF Levinson, SP Hamilton
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 Acute kidney injury in coronary artery bypass surgery (creatinine rise). The EFO term coronary artery bypass, Acute kidney injury, serum creatinine 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:
M Stafford-Smith, YJ Li, JP Mathew, YW Li, Y Ji, BG Phillips-Bute, CA Milano, MF Newman, WE Kraus, MD Kertai, SH Shah, MV Podgoreanu
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 Night sleep phenotypes. The EFO term sleep latency 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:
J Spada, M Scholz, H Kirsten, T Hensch, K Horn, P Jawinski, C Ulke, R Burkhardt, K Wirkner, M Loeffler, U Hegerl, C Sander
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
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
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
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
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
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 Airway imaging phenotypes. The EFO term airway imaging 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:
MH Cho, PJ Castaldi, CP Hersh, BD Hobbs, RG Barr, R Tal-Singer, P Bakke, A Gulsvik, R San José Estépar, EJ Van Beek, HO Coxson, DA Lynch, GR Washko, NM Laird, JD Crapo, TH Beaty, EK Silverman
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 Daytime sleep phenotypes. The EFO term daytime rest 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:
J Spada, M Scholz, H Kirsten, T Hensch, K Horn, P Jawinski, C Ulke, R Burkhardt, K Wirkner, M Loeffler, U Hegerl, C Sander
GWAS: visceral adipose tissue measurement, body mass index
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 Visceral adipose tissue adjusted for BMI. The EFO term visceral adipose tissue measurement, body mass index 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:
CS Fox, Y Liu, CC White, M Feitosa, AV Smith, N Heard-Costa, K Lohman, AD Johnson, MC Foster, DM Greenawalt, P Griffin, J Ding, AB Newman, F Tylavsky, I Miljkovic, SB Kritchevsky, L Launer, M Garcia, G Eiriksdottir, JJ Carr, V Gudnason, TB Harris, LA Cupples, IB Borecki
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 Hearing impairment. The EFO term hearing loss 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:
L Van Laer, JR Huyghe, S Hannula, E Van Eyken, DA Stephan, E Mäki-Torkko, P Aikio, E Fransen, A Lysholm-Bernacchi, M Sorri, MJ Huentelman, G Van Camp
Postmortem human brain tissue from the putamen region of a total of 48 individuals with Alcohol Use Disorder (AUD) and 51 control individuals were taken and RNA extracted from frozen tissue. Sequencing was carried out using the NovaSeq 6000 (Illumina) platform, and gene expression analysis was carried out with respect to AUD and control samples. Gene symbols from Entrez ids are used and Logbase2 FC as provided by the authors are annotated.
Authors:
Lea Zillich, Eric Poisel, Josef Frank, Jerome C Foo, Marion M Friske, Fabian Streit, Lea Sirignano, Stefanie Heilmann-Heimbach, André Heimbach, Per Hoffmann, Franziska Degenhardt, Anita C Hansson, Georgy Bakalkin, Markus M Nöthen, Marcella Rietschel, Rainer Spanagel, Stephanie H Witt
Postmortem human brain tissue from the ventral striatum from postmortem human brain tissue with Alcohol Use Disorder (AUD) region of a total of 48 individuals with Alcohol Use Disorder (AUD) and 51 control individuals were taken and RNA extracted from frozen tissue. Sequencing was carried out using the NovaSeq 6000 (Illumina) platform, and gene expression analysis was carried out with respect to AUD and control samples. Gene symbols from Entrez ids are used and Logbase2 FC as provided by the authors are annotated.
Authors:
Lea Zillich, Eric Poisel, Josef Frank, Jerome C Foo, Marion M Friske, Fabian Streit, Lea Sirignano, Stefanie Heilmann-Heimbach, André Heimbach, Per Hoffmann, Franziska Degenhardt, Anita C Hansson, Georgy Bakalkin, Markus M Nöthen, Marcella Rietschel, Rainer Spanagel, Stephanie H Witt
Differentially expressed genes from RPE compared to Normal Retina
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 Normal RPE were compared to Normal Retina, 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
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
DEG human CN astrocytes CocUD vs control_avg log2FC
Description:
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
GeneWeaver