MORF_DEAF1
Neighborhood of DEAF1
c4 - Computational genesets defined by mining large collections of cancer-oriented microarray data.
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
GCM_DEAF1
Neighborhood of DEAF1
c4 - Computational genesets defined by mining large collections of cancer-oriented microarray data.
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
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.
From the initial set of differentially expressed genes in post mortum nucleus accumbens of chronic heroin and cocaine abusers, this set contains genes downregulated in both cohorts.
Cerebellum Gene Expression Correlates for LM_CUE_SUPPRESS measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The LM_CUE_SUPPRESS measures Suppression of activity in altered context 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
Cerebellum Gene Expression Correlates for LM_CUE_SUPPRESS measured in BXD RI Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The LM_CUE_SUPPRESS measures Suppression of activity in altered context 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 AMCNT180 measured in BXD RI Females & Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The AMCNT180 measures Morphine photocell counts minutes 165-180 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
Neocortex Gene Expression Correlates for HAND_4HOURS measured in BXD RI Females obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. 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
Neocortex Gene Expression Correlates for HAND_6HOURS measured in BXD RI Females obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The HAND_6HOURS measures Handling induced convulsions 6 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
Neocortex Gene Expression Correlates for HIC_SCORE measured in BXD RI Females obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The HIC_SCORE measures Handling induced convulsion score 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
QTL for alcohol preference locus on Chr7 at D7Mit105 (126.73 Mbp , Build 37)
Description:
alcohol preference locus spans 101.73 - 151.73 Mbp (NCBI Build 37) on Chr7. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
alcohol preference locus 14, female specific at D7Mit105 with a LOD score of 1.84 (p < 0.004) spans and preference correlation of 0.591 101.73 - 151.73 Mbp (NCBI Build 37) on Chr7. 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 home cage activity on Chr7 at D7Mit12 (129.57 Mbp , Build 37)
Description:
METH responses for home cage activity spans 104.57 - 154.57 Mbp (NCBI Build 37) on Chr7. 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 Chr7 at Xmv76 (137.02 Mbp , Build 37)
Description:
METH responses for body temperature spans 112.02 - 162.02 Mbp (NCBI Build 37) on Chr7. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Chronic cocaine - Cocaine-paired (conditioned place preference) vs. Control (saline or cocaine-non-paired) DNA microarray All genes on microarray presented After the pre-conditioning phase where animals were allowed access to either compartment for 15 minutes for 4 consecutive days, the conditioning phase for the cocaine-paired groups and cocaine non-paired groups began, consisting of eight subsequent daily sessions. For both groups, cocaine (10 mg / kg) or saline injections were administered on alternate days. For the cocaine-paired groups, rats were immediately placed in one of the two compartments for 30 min with the door in place restricting a z transformation followed by z test and anova followed by Student-Newman-Keuls' post hoc test. Gene expression profile was assessed 24 h after the last conditioning session that corresponded to 48 h after last cocaine exposure, when drug has been eliminated from the body and transient transcriptional changes are likely to be minimal. Therefore, changes in gene expression at this time-point are likely to reflect longer lasting adaptations that may account for maintenance of cocaine-induced memories. The complete lists of normalized gene expression values for the hippocampus of saline-treated, cocaine non-paired and cocaine-paired groups are presented. Analyses revealed that 214 transcripts were differentially regulated in the hippocampus of cocaine-paired rats vs. non-paired and saline-treated controls. Cocaine-induced conditioned place preference caused significant increases in the expression of 151 genes and caused decreases in the expression of 63 genes. (NIF Table ID 130.1 [83])
Authors:
Krasnova IN, Li SM, Wood WH, McCoy MT, Prabhu VV, Becker KG, Katz JL, Cadet JL
Chronic cocaine - Cocaine-paired (conditioned place preference) vs. Control (saline or cocaine-non-paired) DNA microarray All genes on microarray presented After the pre-conditioning phase where animals were allowed access to either compartment for 15 minutes for 4 consecutive days, the conditioning phase for the cocaine-paired groups and cocaine non-paired groups began, consisting of eight subsequent daily sessions. For both groups, cocaine (10 mg / kg) or saline injections were administered on alternate days. For the cocaine-paired groups, rats were immediately placed in one of the two compartments for 30 min with the door in place restricting a z transformation followed by z test and anova followed by Student-Newman-Keuls' post hoc test. Gene expression profile was assessed 24 h after the last conditioning session that corresponded to 48 h after last cocaine exposure, when drug has been eliminated from the body and transient transcriptional changes are likely to be minimal. Therefore, changes in gene expression at this time-point are likely to reflect longer lasting adaptations that may account for maintenance of cocaine-induced memories. The complete lists of normalized gene expression values for the frontal cortex of saline-treated, cocaine non-paired and cocaine-paired groups are presented. Differences in the expression of 39 transcripts in the frontal cortex were related to the conditioned place preference paradigm. These include increases in the level of 22 genes and decreases in 17 genes. (NIF Table ID 130.3 [83.5])
Authors:
Krasnova IN, Li SM, Wood WH, McCoy MT, Prabhu VV, Becker KG, Katz JL, Cadet JL
Chronic cocaine - Cocaine vs. Control DNA microarray Change in gene expression Cocaine users (n = 10) exhibited a positive toxicology for cocaine and / or its metabolites. Control subjects (n = 10) were matched pair-wise with cocaine users for manner of death, age, gender, and race. Of the 20 subjects, two cocaine and two control subjects tested positive for subintoxicating doses of alcohol (g / dL < or = to 0.07) but did not exhibit common signs of chronic alcohol abuse, and alcohol did not have predictive value in hierarchical clustering of subjects based on gene express Affymetrix Microarray Suite 5.0 software package. Subjects were analyzed in pairs, comparing each cocaine sample with its matched control. Significant differences between subject pairs were calculated using the Wilcoxon signed rank test (p < or = to 0.05). Post-hoc examination confirmed the statistical significance of differential expression for the majority of transcripts (Mann-Whitney U-test, p < or = to 0.05; data not shown). Transcripts increased or decreased in the majority (> or = to 6 of 10) of pairs, representing only 0.2% of the total transcripts, were considered differentially expressed. Transcripts meeting this criterion were examined posthoc for statistical significance using Mann?Whitney U-tests (p < or = to 0.05). (NIF Table ID 145 [114])
Chronic ethanol - Ethanol vs. Control DNA microarray Change in gene expression - Class II Alcoholics were classified based on the quantity of alcohol consumed, according to the National Health and Medical Research Council (NHMRC) (>80 g of alcohol per day), instead of the criteria established by the American Psychiatric Association (DSM-IV) or the World Health Organization (ICD-10). Many alcoholic patients in this study consumed significantly more than 80 g / day for most of their adult life. Cerebral atrophy was observed in three alcoholic cases. All alcoholic cases included in our Axon GenePix 4.0 software; partial least squares (PLS) statistical procedure; linear discriminant analysis (LDA) procedure for prediction analysis. PLS and LDA analysis were performed using in JMP IN software; principal component analysis (PCA) used STATISTICA software. Results reflect the combined dataset: Class I genes were qualitatively different, that is, they were predominantly detected in one group but not the other. They represent those that were more likely turned off or turned on as a result of alcohol abuse. Class II genes were consistently detected in both groups. They represent consistently expressed genes for which quantitative differences in expression could be determined. (NIF Method ID 157)
Genes associated with Homo sapiens that interact with the MeSH term 'methylselenic acid' (C008493). Incorporates data from 2 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Papio that interact with the MeSH term 'Cocaine' (D003042). Incorporates data from 5 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Cycloheximide' (D003513). Incorporates data from 1 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
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