Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "Homo sapiens" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is miRTarBase.
gene2pc v. 0.1.0
Last updated 2015.08.31
Postmortem human brain tissue from the caudate nucleus 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
The dataset used in this study (Bulk RNA-Seq) was previously published and can be found at NCBI GEO (GSE182321), this analysis was conducted by GEO2R to compare control and OUD samples, only top differentially expressed genes are reported. To understand mechanisms and identify potential targets for intervention in the current crisis of opioid use disorder (OUD), postmortem brains represent an under-utilized resource. To refine previously reported gene signatures of neurobiological alterations in OUD from the dorsolateral prefrontal cortex (Brodmann Area 9, BA9), we explored the role of microRNAs (miRNA) as powerful epigenetic regulators of gene function.
The dataset used in this study (Bulk RNA-Seq) was previously published and can be found at NCBI GEO (GSE182321), this analysis was conducted by GEO2R to compare control and OUD samples, only top differentially expressed genes are reported. To understand mechanisms and identify potential targets for intervention in the current crisis of opioid use disorder (OUD), postmortem brains represent an under-utilized resource. To refine previously reported gene signatures of neurobiological alterations in OUD from the dorsolateral prefrontal cortex (Brodmann Area 9, BA9), we explored the role of microRNAs (miRNA) as powerful epigenetic regulators of gene function.
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
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
Differential gene expression between CS15 and CS22 - Log2FC
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17, and CS22. Here the differential expression comparison between CS15 and CS22 is shown. Gene expressions values with log to the base 2, FC are presented with P-Adj <0.05. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS15 and CS22 - Adj-P value
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17 and CS22. Here the differential expression comparison between CS15 and CS22 is shown. Gene expressions values, Ensembl Gene ids and the corresponding Adjusted P value are presented. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS13 and CS22 - Log2FC
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17, and CS22. Here the differential expression comparison between CS13 and CS22 is shown. Gene expressions values with log to the base 2, FC are presented with P-Adj <0.05. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS13 and CS22 - Adj-P value
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17 and CS22. Here the differential expression comparison between CS13 and CS22 is shown. Gene expressions values, Ensembl Gene ids and the corresponding Adjusted P value are presented. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS17 and CS22 - Log2FC
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17, and CS22. Here the differential expression comparison between CS17 and CS22 is shown. Gene expressions values with log to the base 2, FC are presented with P-Adj <0.05. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS14 and CS22 - Adj-P value
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17 and CS22. Here the differential expression comparison between CS14 and CS22 is shown. Gene expressions values, Ensembl Gene ids and the corresponding Adjusted P value are presented. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS14 and CS22 - Log2FC
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17, and CS22. Here the differential expression comparison between CS14 and CS22 is shown. Gene expressions values with log to the base 2, FC are presented with P-Adj <0.05. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS14 and CS22 - Adj-P value
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17 and CS22. Here the differential expression comparison between CS14 and CS22 is shown. Gene expressions values, Ensembl Gene ids and the corresponding Adjusted P value are presented. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Opioid controls_human_ dorsolateral prefrontal cortex and 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
Opioid controls_human_ dorsolateral prefrontal cortex and nucleus accumbens_qvalue
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_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
Opioid_human_dorsolateral prefrontal cortex_reanalysis of Corradin et al. 2022_log2FC
Description:
doi: https://doi.org/10.1101/2024.01.12.24301153. This study is a re-analysis of publicly available data and a meta-analysis investigating differential gene expression associated with opioid use disorder from Corradin et al. 2022 (PMID: 35301427); Mendez et al. 2021 (PMID: 34385598); Seney et al. 2021 (PMID: 34380600); and Sosnowski et al. 2022 (PMID:36845993 ). All four of these studies used human postmortem dorsolateral prefrontal cortex (DLPFC) brain tissue from donors identified as dying from OOD through toxicology assays administered by forensic scientists and phenotypic evidence of opioid addiction. Each of these independent studies had modest sample sizes (N = 40-153) and compared bulk RNA-seq data from individuals who died from OOD to individuals who died from non–drug use causes.
Opioid_human_dorsolateral prefrontal cortex_reanalysis of Corradin et al. 2022_qvalue
Description:
doi: https://doi.org/10.1101/2024.01.12.24301153. This study is a re-analysis of publicly available data and a meta-analysis investigating differential gene expression associated with opioid use disorder from Corradin et al. 2022 (PMID: 35301427); Mendez et al. 2021 (PMID: 34385598); Seney et al. 2021 (PMID: 34380600); and Sosnowski et al. 2022 (PMID:36845993 ). All four of these studies used human postmortem dorsolateral prefrontal cortex (DLPFC) brain tissue from donors identified as dying from OOD through toxicology assays administered by forensic scientists and phenotypic evidence of opioid addiction. Each of these independent studies had modest sample sizes (N = 40-153) and compared bulk RNA-seq data from individuals who died from OOD to individuals who died from non–drug use causes.
Opioid_human_dorsolateral prefrontal cortex_reanalysis of Mendez et al 2021_log2FC
Description:
doi: https://doi.org/10.1101/2024.01.12.24301153. This study is a re-analysis of publicly available data and a meta-analysis investigating differential gene expression associated with opioid use disorder from Corradin et al. 2022 (PMID: 35301427); Mendez et al. 2021 (PMID: 34385598); Seney et al. 2021 (PMID: 34380600); and Sosnowski et al. 2022 (PMID:36845993 ). All four of these studies used human postmortem dorsolateral prefrontal cortex (DLPFC) brain tissue from donors identified as dying from OOD through toxicology assays administered by forensic scientists and phenotypic evidence of opioid addiction. Each of these independent studies had modest sample sizes (N = 40-153) and compared bulk RNA-seq data from individuals who died from OOD to individuals who died from non–drug use causes.
doi: https://doi.org/10.1101/2024.01.12.24301153. This study is a re-analysis of publicly available data and a meta-analysis investigating differential gene expression associated with opioid use disorder from Corradin et al. 2022 (PMID: 35301427); Mendez et al. 2021 (PMID: 34385598); Seney et al. 2021 (PMID: 34380600); and Sosnowski et al. 2022 (PMID:36845993 ). All four of these studies used human postmortem dorsolateral prefrontal cortex (DLPFC) brain tissue from donors identified as dying from OOD through toxicology assays administered by forensic scientists and phenotypic evidence of opioid addiction. Each of these independent studies had modest sample sizes (N = 40-153) and compared bulk RNA-seq data from individuals who died from OOD to individuals who died from non–drug use causes.
Opioid_human_dorsolateral prefrontal cortex_reanalysis of Seney et al 2021_log2FC
Description:
doi: https://doi.org/10.1101/2024.01.12.24301153. This study is a re-analysis of publicly available data and a meta-analysis investigating differential gene expression associated with opioid use disorder from Corradin et al. 2022 (PMID: 35301427); Mendez et al. 2021 (PMID: 34385598); Seney et al. 2021 (PMID: 34380600); and Sosnowski et al. 2022 (PMID:36845993 ). All four of these studies used human postmortem dorsolateral prefrontal cortex (DLPFC) brain tissue from donors identified as dying from OOD through toxicology assays administered by forensic scientists and phenotypic evidence of opioid addiction. Each of these independent studies had modest sample sizes (N = 40-153) and compared bulk RNA-seq data from individuals who died from OOD to individuals who died from non–drug use causes.
Opioid_human_dorsolateral prefrontal cortex_reanalysis of Seney et al 2021_qvalue
Description:
doi: https://doi.org/10.1101/2024.01.12.24301153. This study is a re-analysis of publicly available data and a meta-analysis investigating differential gene expression associated with opioid use disorder from Corradin et al. 2022 (PMID: 35301427); Mendez et al. 2021 (PMID: 34385598); Seney et al. 2021 (PMID: 34380600); and Sosnowski et al. 2022 (PMID:36845993 ). All four of these studies used human postmortem dorsolateral prefrontal cortex (DLPFC) brain tissue from donors identified as dying from OOD through toxicology assays administered by forensic scientists and phenotypic evidence of opioid addiction. Each of these independent studies had modest sample sizes (N = 40-153) and compared bulk RNA-seq data from individuals who died from OOD to individuals who died from non–drug use causes.
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