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
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
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 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
Genome-wide association studies are conducted of two human cohorts, one group demonstrating nicotine dependence and another successfully quitting smoking. Study shows that some genetic components associated with the ability to quit overlap while many do not overlap. To perform the study, DNA samples were obtained from NIH volunteers and the allelic frequencies of the samples were analyzed using Affymetrix array analysis. This gene set comprises 290 genes associated with nicotine dependence.
Authors:
Drgon T, Montoya I, Johnson C, Liu QR, Walther D, Hamer D, Uhl GR
Hippocampus Gene Expression Correlates for CONSTRICT measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The CONSTRICT measures Morphine Response Severity of abdominal constriction 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
Cerebellum Gene Expression Correlates for OF_HAB_RATIO measured in BXD RI Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The OF_HAB_RATIO measures Open Field - Habituation ratio (First:Last intervals) under the domain Basal Behavior. 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 ADUL_RMS_BRDU measured in BXD RI Females obtained using INIA Brain mRNA M430 (Jun06) RMA. The ADUL_RMS_BRDU measures Neurogenesis- BrdU labeled new neurons in Adult Rostral Migratory Stream 1 hr post BrdU under the domain Neurogenesis. 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
Striatum Gene Expression Correlates for HAND_4HOURS measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The HAND_4HOURS measures Handling induced convulsions 4 hrs after ethanol under the domain Ethanol HIC. 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
Striatum Gene Expression Correlates for HAND_4HOURS measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The HAND_4HOURS measures Handling induced convulsions 4 hrs after ethanol under the domain Ethanol HIC. 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 LD_DISTANCE measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LD_DISTANCE measures Light-Dark Box Total distance traveled in light and dark compartments under the domain Basal Behavior. 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 LD_DISTANCE measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LD_DISTANCE measures Light-Dark Box Total distance traveled in light and dark compartments under the domain Basal Behavior. 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 LM_BASELINE measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_BASELINE measures Baseline activity in fear conditioning apparatus under the domain Basal Behavior. 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 LM_BASELINE measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_BASELINE measures Baseline activity in fear conditioning apparatus under the domain Basal Behavior. 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 LM_PAIR1 measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_PAIR1 measures Activity during 1st tone shock pairing under the domain Basal Behavior. 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 LM_PAIR1 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_PAIR1 measures Activity during 1st tone shock pairing under the domain Basal Behavior. 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 LM_PAIR2 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_PAIR2 measures Activity during 2ndtone shock pairing under the domain Basal Behavior. 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
Neocortex Gene Expression Correlates for MDMA_ACT_MDA_1 measured in BXD RI Females obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The MDMA_ACT_MDA_1 measures Locomotor response of 10 mg/kg MDMA injected on Day 2 under the domain MDMA. 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 SALIVA measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The SALIVA measures Morphine - Salivation 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
QTL for METH responses for body temperature on Chr19 at Pomc-2 (14.21 Mbp , Build 37)
Description:
METH responses for body temperature spans 0.00 - 39.21 Mbp (NCBI Build 37) on Chr19. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for METH responses for body temperature on Chr19 at Lpc1 (23.27 Mbp , Build 37)
Description:
METH responses for body temperature spans 0.00 - 48.27 Mbp (NCBI Build 37) on Chr19. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for alcohol preference locus on Chr19 at D19Mit46 (29.54 Mbp , Build 37)
Description:
alcohol preference locus spans 4.54 - 54.54 Mbp (NCBI Build 37) on Chr19. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for alcohol preference locus on Chr19 at D19Mit46 (29.54 Mbp , Build 37)
Description:
alcohol preference locus spans 4.54 - 54.54 Mbp (NCBI Build 37) on Chr19. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
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