Chronic nicotine - Schizophrenic vs. Control Quantitative reverse transcriptase-polymerase chain reaction Change in gene expression Postmortem parameters, such as age, sex, ethnicity, medication history, mental illness status, cigarette smoking history, and alcohol use, were evaluated through hospital, autopsy, and neuropathology reports. Family members and physicians were also interviewed to detail the smoking and alcohol history of the subject, including packs of cigarettes smoked per day, and the quantity and type of alcohol consumed. All of the subjects who had used alcohol prior to death had consumed no more than two dr two-way ANOVA; Fisher's exact test; Student's t test Values for each sample were normalized to GAPDH. Relative expression values were log10 transformed and differences in mean gene expression were determined using a Student's t test (P < 0.05). For QRT-PCR results, mean relative mRNA amounts +/- standard error of the mean (SEM) for each experimental group were graphed in Sigma Plot 2000. (NIF Table ID 215 [131])
Authors:
Mexal S, Frank M, Berger R, Adams CE, Ross RG, Freedman R, Leonard S
Chronic nicotine - Nicotine vs. Control Quantitative reverse transcriptase-polymerase chain reaction Change in gene expression Postmortem parameters, such as age, sex, ethnicity, medication history, mental illness status, cigarette smoking history, and alcohol use, were evaluated through hospital, autopsy, and neuropathology reports. Family members and physicians were also interviewed to detail the smoking and alcohol history of the subject, including packs of cigarettes smoked per day, and the quantity and type of alcohol consumed. All of the subjects who had used alcohol prior to death had consumed no more than two dr two-way ANOVA; Fisher's exact test; Student's t test Values for each sample were normalized to GAPDH. Relative expression values were log10 transformed and differences in mean gene expression were determined using a Student's t test (P < 0.05). For QRT-PCR results, mean relative mRNA amounts +/- standard error of the mean (SEM) for each experimental group were graphed in Sigma Plot 2000. (NIF Table ID 215 [128])
Authors:
Mexal S, Frank M, Berger R, Adams CE, Ross RG, Freedman R, Leonard S
Chronic nicotine - Nicotine vs. Control Quantitative reverse transcriptase-polymerase chain reaction Change in gene expression Postmortem parameters, such as age, sex, ethnicity, medication history, mental illness status, cigarette smoking history, and alcohol use, were evaluated through hospital, autopsy, and neuropathology reports. Family members and physicians were also interviewed to detail the smoking and alcohol history of the subject, including packs of cigarettes smoked per day, and the quantity and type of alcohol consumed. All of the subjects who had used alcohol prior to death had consumed no more than two dr two-way ANOVA; Fisher's exact test; Student's t test Values for each sample were normalized to GAPDH. Relative expression values were log10 transformed and differences in mean gene expression were determined using a Student's t test (P < 0.05). For QRT-PCR results, mean relative mRNA amounts +/- standard error of the mean (SEM) for each experimental group were graphed in Sigma Plot 2000. (NIF Table ID 215 [130])
Authors:
Mexal S, Frank M, Berger R, Adams CE, Ross RG, Freedman R, Leonard S
None - Schizophrenic vs. Control Quantitative reverse transcriptase-polymerase chain reaction Change in gene expression Postmortem parameters, such as age, sex, ethnicity, medication history, mental illness status, cigarette smoking history, and alcohol use, were evaluated through hospital, autopsy, and neuropathology reports. Family members and physicians were also interviewed to detail the smoking and alcohol history of the subject, including packs of cigarettes smoked per day, and the quantity and type of alcohol consumed. All of the subjects who had used alcohol prior to death had consumed no more than two dr two-way ANOVA; Fisher's exact test; Student's t test Values for each sample were normalized to GAPDH. Relative expression values were log10 transformed and differences in mean gene expression were determined using a Student's t test (P < 0.05). For QRT-PCR results, mean relative mRNA amounts +/- standard error of the mean (SEM) for each experimental group were graphed in Sigma Plot 2000. (NIF Method ID 129)
Authors:
Mexal S, Frank M, Berger R, Adams CE, Ross RG, Freedman R, Leonard S
Chronic nicotine - Nicotine vs. Control Quantitative reverse transcriptase-polymerase chain reaction Change in gene expression Postmortem parameters, such as age, sex, ethnicity, medication history, mental illness status, cigarette smoking history, and alcohol use, were evaluated through hospital, autopsy, and neuropathology reports. Family members and physicians were also interviewed to detail the smoking and alcohol history of the subject, including packs of cigarettes smoked per day, and the quantity and type of alcohol consumed. All of the subjects who had used alcohol prior to death had consumed no more than two dr two-way ANOVA; Fisher's exact test; Student's t test Values for each sample were normalized to GAPDH. Relative expression values were log10 transformed and differences in mean gene expression were determined using a Student's t test (P < 0.05). For QRT-PCR results, mean relative mRNA amounts +/- standard error of the mean (SEM) for each experimental group were graphed in Sigma Plot 2000. (NIF Method ID 130)
Authors:
Mexal S, Frank M, Berger R, Adams CE, Ross RG, Freedman R, Leonard S
Chronic nicotine - Schizophrenic vs. Control Quantitative reverse transcriptase-polymerase chain reaction Change in gene expression Postmortem parameters, such as age, sex, ethnicity, medication history, mental illness status, cigarette smoking history, and alcohol use, were evaluated through hospital, autopsy, and neuropathology reports. Family members and physicians were also interviewed to detail the smoking and alcohol history of the subject, including packs of cigarettes smoked per day, and the quantity and type of alcohol consumed. All of the subjects who had used alcohol prior to death had consumed no more than two dr two-way ANOVA; Fisher's exact test; Student's t test Values for each sample were normalized to GAPDH. Relative expression values were log10 transformed and differences in mean gene expression were determined using a Student's t test (P < 0.05). For QRT-PCR results, mean relative mRNA amounts +/- standard error of the mean (SEM) for each experimental group were graphed in Sigma Plot 2000. (NIF Method ID 131)
Authors:
Mexal S, Frank M, Berger R, Adams CE, Ross RG, Freedman R, Leonard S
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "GKAP/Homer scaffold activity", which is defined as "Functions as a physical support bridging the N-methyl-D-aspartate receptor-PSD-95-GKAP complex and the mGluR-Homer complex, which are involved in receptor signaling in synapses." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "postsynaptic density", which is defined as "An electron dense network of proteins within and adjacent to the postsynaptic membrane of an asymmetric, neuron-neuron synapse. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.12.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
"The clustering process in which postsynaptic density protein 95 (PSD-95) molecules are localized to distinct domains in the cell membrane. PSD-95 is mostly located in the post synaptic density of neurons, and is involved in anchoring synaptic proteins." [GOC:BHF, GOC:sjp, PMID:10433269]
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "postsynaptic density protein 95 clustering", which is defined as "The clustering process in which postsynaptic density protein 95 (PSD-95) molecules are localized to distinct domains in the cell membrane. PSD-95 is mostly located in the post synaptic density of neurons, and is involved in anchoring synaptic proteins." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "postsynaptic density protein 95 clustering", which is defined as "The clustering process in which postsynaptic density protein 95 (PSD-95) molecules are localized to distinct domains in the cell membrane. PSD-95 is mostly located in the post synaptic density of neurons, and is involved in anchoring synaptic proteins." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.12.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Neocortex Gene Expression Correlates for LM_PAIR2 measured in BXD RI Females & Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. 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 LM_PAIR2 measured in BXD RI Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The LM_PAIR2 measures Activity during 2nd 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
A list of genes whose transcript abundance in the PFC changed significantly 4 hours after an acute dose of ethanol (1.8 g/kg). This list was generated using Fisher's Combined Probability test to analyze saline vs ethanol S-scores across B6 and D2 inbred strains (n=3) and 27 BXD RI lines (n=1). Statistical significance was determined using 1,000 permutations of S-score data and selecting for probe-sets with q-values < 0.05. Aaron Wolen 5-26-10.
Authors:
Wolen AR, Phillips CA, Langston MA, Putman AH, Vorster PJ, Bruce NA, York TP, Williams RW, Miles MF
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).
None - Basal gene expression profiles between C57BL/6J, DBA/2J, 129P3/J, and SWR/J strains DNA microarray Change in gene expression Two-way analysis of variance (ANOVA). 3,457 probe sets (corresponded to 2,870 different transcripts) with significant inter-strain differences (differ by at least 1.2-fold) - False discovery rate [FDR] < 1%, , rank > 3. Such a large disparity in the mouse striatal transcriptome was estimated by comparing nine array replicates prepared per strain from all of the treatment groups. More than half of the identified probe sets exhibited markedly significant results (1,735 with rank > 7). (NIF Method ID 84.1)
Authors:
Korostynski M, Piechota M, Kaminska D, Solecki W, Przewlocki R
Genes associated with Homo sapiens that interact with the MeSH term 'Copper Sulfate' (D019327). Incorporates data from 72 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 'Plant Extracts' (D010936). Incorporates data from 489 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 'Aspirin' (D001241). Incorporates data from 43 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 'Diazinon' (D003976). Incorporates data from 2 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
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