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 middle facial morphology traits (quantitative measurement). The EFO term nose morphology measurement 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:
K Adhikari, M Fuentes-Guajardo, M Quinto-Sánchez, J Mendoza-Revilla, J Camilo Chacón-Duque, V Acuña-Alonzo, C Jaramillo, W Arias, RB Lozano, GM Pérez, J Gómez-Valdés, H Villamil-Ramírez, T Hunemeier, V Ramallo, CC Silva de Cerqueira, M Hurtado, V Villegas, V Granja, C Gallo, G Poletti, L Schuler-Faccini, FM Salzano, MC Bortolini, S Canizales-Quinteros, M Cheeseman, J Rosique, G Bedoya, F Rothhammer, D Headon, R González-José, D Balding, A Ruiz-Linares
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 facial morphology traits (multivariate analysis). The EFO term facial morphology measurement 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:
K Adhikari, M Fuentes-Guajardo, M Quinto-Sánchez, J Mendoza-Revilla, J Camilo Chacón-Duque, V Acuña-Alonzo, C Jaramillo, W Arias, RB Lozano, GM Pérez, J Gómez-Valdés, H Villamil-Ramírez, T Hunemeier, V Ramallo, CC Silva de Cerqueira, M Hurtado, V Villegas, V Granja, C Gallo, G Poletti, L Schuler-Faccini, FM Salzano, MC Bortolini, S Canizales-Quinteros, M Cheeseman, J Rosique, G Bedoya, F Rothhammer, D Headon, R González-José, D Balding, A Ruiz-Linares
V$OSF2_Q6
Genes with promoter regions [-2kb,2kb] around transcription start site containing the motif ACCACANM which matches annotation for RUNX2: runt-related transcription factor 2
c3 - Motif genesets based on conserved cis-regulatory motifs from a comparative analysis of the human, mouse, rat, and dog genomes.
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
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 Periodontal microbiota. The EFO term periodontitis 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:
K Divaris, KL Monda, KE North, AF Olshan, EM Lange, K Moss, SP Barros, JD Beck, S Offenbacher
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 lower facial morphology traits (quantitative measurement). The EFO term lip morphology measurement, chin morphology measurement 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:
K Adhikari, M Fuentes-Guajardo, M Quinto-Sánchez, J Mendoza-Revilla, J Camilo Chacón-Duque, V Acuña-Alonzo, C Jaramillo, W Arias, RB Lozano, GM Pérez, J Gómez-Valdés, H Villamil-Ramírez, T Hunemeier, V Ramallo, CC Silva de Cerqueira, M Hurtado, V Villegas, V Granja, C Gallo, G Poletti, L Schuler-Faccini, FM Salzano, MC Bortolini, S Canizales-Quinteros, M Cheeseman, J Rosique, G Bedoya, F Rothhammer, D Headon, R González-José, D Balding, A Ruiz-Linares
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "core-binding factor complex", which is defined as "A heterodimeric transcription factor complex that contains an alpha subunit (Runx1, Runx2 or Runx3 in human) that binds DNA and a non-DNA-binding beta subunit (CBFbeta), and binds to a consensus sequence 5'-YGYGGTY-3' found in several enhancers and promoters; the beta subunit enhances the DNA binding of the alpha subunit." 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 "core-binding factor complex", which is defined as "A heterodimeric transcription factor complex that contains an alpha subunit (Runx1, Runx2 or Runx3 in human) that binds DNA and a non-DNA-binding beta subunit (CBFbeta), and binds to a consensus sequence 5'-YGYGGTY-3' found in several enhancers and promoters; the beta subunit enhances the DNA binding of the alpha subunit." 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
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "core-binding factor complex", which is defined as "A heterodimeric transcription factor complex that contains an alpha subunit (Runx1, Runx2 or Runx3 in human) that binds DNA and a non-DNA-binding beta subunit (CBFbeta), and binds to a consensus sequence 5'-YGYGGTY-3' found in several enhancers and promoters; the beta subunit enhances the DNA binding of the alpha subunit." 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
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
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 ACTI15_SAL measured in BXD RI Females obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The ACTI15_SAL measures Distance traveled (cm) during the third five minute bin after saline 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
Hippocampus Gene Expression Correlates for C1HCOUNT30 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HCOUNT30 measures Open Field locomotion 15-30 min post cocaine 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
Hippocampus Gene Expression Correlates for C1HCOUNT45 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HCOUNT45 measures Open Field locomotion 30-45 min post cocaine 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
Hippocampus Gene Expression Correlates for C1HCOUNT60 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HCOUNT60 measures Open Field locomotion 45-60 min post cocaine 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
Hippocampus Gene Expression Correlates for C1HDIS60 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The C1HDIS60 measures Open Field locomotion (cm) 45-60 min post cocaine 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
Whole Brain Gene Expression Correlates for HP_LATENCY measured in BXD RI Females & Males obtained using INIA Brain mRNA M430 (Jun06) RMA. The HP_LATENCY measures Thermal Nociception Hot Plate Latency 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 LOC_CHCL_ACOUNT_3 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LOC_CHCL_ACOUNT_3 measures Cocaine TOTAL locomotion (activity beam breaks) 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
Hippocampus Gene Expression Correlates for LOC_CHCL_ADIST_3 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LOC_CHCL_ADIST_3 measures Cocaine TOTAL locomotion ( cm in 1 hr) 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
Striatum Gene Expression Correlates for NEPDIST15 measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The NEPDIST15 measures Novel environment distance (cm) travelled 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
Striatum Gene Expression Correlates for NEPDIST15 measured in BXD RI Males obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The NEPDIST15 measures Novel environment distance (cm) travelled minutes 0-15 under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
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