GWAS: metastasis measurement, date of diagnosis, osteosarcoma
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 Metastasis at diagnosis in osteosarcoma. The EFO term metastasis measurement, date of diagnosis, osteosarcoma 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 Mirabello, R Koster, BS Moriarity, LG Spector, PS Meltzer, J Gary, MJ Machiela, N Pankratz, OA Panagiotou, D Largaespada, Z Wang, JM Gastier-Foster, R Gorlick, C Khanna, SR de Toledo, AS Petrilli, A Patiño-Garcia, L Sierrasesúmaga, F Lecanda, IL Andrulis, JS Wunder, N Gokgoz, M Serra, C Hattinger, P Picci, K Scotlandi, AM Flanagan, R Tirabosco, MF Amary, D Halai, ML Ballinger, DM Thomas, S Davis, DA Barkauskas, N Marina, L Helman, GM Otto, KL Becklin, NK Wolf, MT Weg, M Tucker, S Wacholder, JF Fraumeni, NE Caporaso, JF Boland, BD Hicks, A Vogt, L Burdett, M Yeager, RN Hoover, SJ Chanock, SA Savage
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 Alzheimer's disease biomarkers. The EFO term amyloid-beta measurement, Alzheimers disease 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:
VK Ramanan, SL Risacher, K Nho, S Kim, S Swaminathan, L Shen, TM Foroud, H Hakonarson, MJ Huentelman, PS Aisen, RC Petersen, RC Green, CR Jack, RA Koeppe, WJ Jagust, MW Weiner, AJ Saykin
Cerebellum differential expression analysis of genotype by time effects in Pax6 mice and controls. This set contains genes for which there is an additive effect of the mutation and linear increase in both mutant and wild types through time.
Activation of the mesolimbic dopamine reward pathway by acute ethanol produces reinforcement and changes in gene expression that appear to be crucial to the molecular basis for adaptive behaviors and addiction. The inbred mouse strains DBA/2J and C57BL/6J exhibit contrasting acute behavioral responses to ethanol. We used oligonucleotide microarrays and bioinformatics methods to characterize patterns of gene expression in three brain regions of the mesolimbic reward pathway of these strains. Expression profiling included examination of both differences in gene expression 4 h after saline injection or acute ethanol (2 g/kg). Using a rigorous stepwise method for microarray analysis, we identified 788 genes differentially expressed in control DBA/2J versus C57BL/6J mice and 307 ethanol-regulated genes in the nucleus accumbens, prefrontal cortex, and ventral tegmental area. There were strikingly divergent patterns of ethanol-responsive gene expression in the two strains. Ethanol-responsive genes also showed clustering at discrete chromosomal regions, suggesting local chromatin effects in regulation. Ethanol-regulated genes were generally related to neuroplasticity, but regulation of discrete functional groups and pathways was brain region specific: glucocorticoid signaling, neurogenesis, and myelination in the prefrontal cortex; neuropeptide signaling and developmental genes, including factor Bdnf, in the nucleus accumbens; and retinoic acid signaling in the ventral tegmental area. Bioinformatics analysis identified several potential candidate genes for quantitative trait loci linked to ethanol behaviors, further supporting a role for expression profiling in identifying genes for complex traits. Brain region-specific changes in signaling and neuronal plasticity may be critical components in development of lasting ethanol behavioral phenotypes such as dependence, sensitization, and craving.
Examination of changes in gene expression induced by repeated administration of the mGlu5 antagonists MPEP and MTEP. Male Wistar rats (n=5 per treatment group) were administered MPEP (10 mg/kg), MTEP (10 mg/kg) or vehicle intraperitoneally twice daily for 5 days.
To monitor the expression levels of a large number of genes and to identify genes not previously implicated in traumatic brain injury pathophysiology, a high-density oligonucleotide array containing 8,800 genes was interrogated. RNA samples were prepared from ipsilateral hippocampi 3 hr and 24 hr following lateral cortical impact injury and compared to samples from sham-operated controls.
Authors:
Matzilevich DA, Rall JM, Moore AN, Grill RJ, Dash PK
Using results from genome wide association studies of nicotine dependent individuals who were successful in abstaining from cigarette smoking, study nominates genes important in nicotine dependence and in smoking cessation. Results were obtained using SNP allele frequency assessments of DNA prepared from nicotine-dependent European-American smoking cessation trial participants and control individuals. This Gene set comprises the 55 nicotine dependence genes found.
Authors:
Uhl GR, Liu QR, Drgon T, Johnson C, Walther D, Rose JE
The nuclear accumbens (NA) and amygdale (Amyg) of inbred alcohol-preferring mice were examined for differential gene expression and it findings suggest that changes in gene expression in the ACB of iP rats are associated with the reinforcing effects of ethanol (EtOH). This gene set comprises 201 genes that were significantly expressed in the NA during the experiment.
A list of the 307 genes found to be upregulated or downregulated by ethanol in PFC, VTA or NA of B6 or D2 mice. ID number represents cluster membership from Figure 4.
Authors:
Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Sikela JM, Williams RW, Miles MF
Cerebellum Gene Expression Correlates for TAILCLIP_LAT_SEC measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The TAILCLIP_LAT_SEC measures Mechanical Nociception - Tail Clip Test under the domain Pain. 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 TAILCLIP_LAT_SEC measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The TAILCLIP_LAT_SEC measures Mechanical Nociception - Tail Clip Test under the domain Pain. 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_SUPPRESSION measured in BXD RI Females obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_SUPPRESSION measures Cue Conditioning - Activity suppression after 3rd 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_SUPPRESSION measured in BXD RI Females obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_SUPPRESSION measures Cue Conditioning - Activity suppression after 3rd tone/shock pairing under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Cerebellum Gene Expression Correlates for MORPH_VCOUNT_2 measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The MORPH_VCOUNT_2 measures Morphine TOTAL vertical activity counts 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 PCT_TIME_OPEN measured in BXD RI Females & Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The PCT_TIME_OPEN measures Percentage of time into open arms of plus maze under the domain Ethanol. 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 ROTAETHA_TIME measured in BXD RI Females & Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The ROTAETHA_TIME measures Mean time on rotarod following ethanol under the domain Ethanol. 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 SVCOUNT45 measured in BXD RI Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The SVCOUNT45 measures Open Field Rears 30-45 min post saline under the domain Cocaine. 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 TIME_OPEN_SAL measured in BXD RI Females & Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The TIME_OPEN_SAL measures Amount of time in open arms of plus maze under the domain Ethanol. 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 AMCNT15 measured in BXD RI Females obtained using INIA Brain mRNA M430 (Jun06) RMA. The AMCNT15 measures Morphine photocell counts minutes 0-15 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 AMCNT15 measured in BXD RI Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The AMCNT15 measures Morphine photocell counts minutes 0-15 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 POSTURE measured in BXD RI Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The POSTURE measures Morphine - Postural Effects 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 VERCNT105 measured in BXD RI Females & Males obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The VERCNT105 measures Morphine vertical activity counts minutes 90-105 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 VERCNT105 measured in BXD RI Females obtained using SJUT Cerebellum mRNA M430 (Mar05) RMA. The VERCNT105 measures Morphine vertical activity counts minutes 90-105 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
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