Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "ATM pathway" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is pid.
gene2pc 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 Response to metformin in type 2 diabetes (glycemic). The EFO term response to metformin 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 Zhou, C Bellenguez, CC Spencer, AJ Bennett, RL Coleman, R Tavendale, SA Hawley, LA Donnelly, C Schofield, CJ Groves, L Burch, F Carr, A Strange, C Freeman, JM Blackwell, E Bramon, MA Brown, JP Casas, A Corvin, N Craddock, P Deloukas, S Dronov, A Duncanson, S Edkins, E Gray, S Hunt, J Jankowski, C Langford, HS Markus, CG Mathew, R Plomin, A Rautanen, SJ Sawcer, NJ Samani, R Trembath, AC Viswanathan, NW Wood, LW Harries, AT Hattersley, AS Doney, H Colhoun, AD Morris, C Sutherland, DG Hardie, L Peltonen, MI McCarthy, RR Holman, CN Palmer, P Donnelly, ER Pearson
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 Gastric cancer. The EFO term gastric carcinoma 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:
H Helgason, T Rafnar, HS Olafsdottir, JG Jonasson, A Sigurdsson, SN Stacey, A Jonasdottir, L Tryggvadottir, K Alexiusdottir, A Haraldsson, L le Roux, J Gudmundsson, H Johannsdottir, A Oddsson, A Gylfason, OT Magnusson, G Masson, T Jonsson, H Skuladottir, DF Gudbjartsson, U Thorsteinsdottir, P Sulem, K Stefansson
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 Gastric adenocarcinoma (histologically verified). The EFO term gastric adenocarcinoma 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:
H Helgason, T Rafnar, HS Olafsdottir, JG Jonasson, A Sigurdsson, SN Stacey, A Jonasdottir, L Tryggvadottir, K Alexiusdottir, A Haraldsson, L le Roux, J Gudmundsson, H Johannsdottir, A Oddsson, A Gylfason, OT Magnusson, G Masson, T Jonsson, H Skuladottir, DF Gudbjartsson, U Thorsteinsdottir, P Sulem, K Stefansson
Genes that are downregulated directly or indirectly by Mir302b in MDA-MB-231 or BT-549 cells made cisplatin-sensitive by overexpression of Mir302b. HGNC identifiers were manually assigned. Therapy:Cisplatin. Response Type:Sensitive
Authors:
Cataldo A, Cheung DG, Balsari A, Tagliabue E, Coppola V, Iorio MV, Palmieri D, Croce CM
Genes directly or indirectly downregulated in T47D cells made cisplatin sensitive by overexpression of mir-302b. HGNC identifiers were manually assigned. Therapy:Cisplatin. Response Type:Sensitive
Authors:
Cataldo A, Cheung DG, Balsari A, Tagliabue E, Coppola V, Iorio MV, Palmieri D, Croce CM
GNF2_ATM
Neighborhood of ATM
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_ATM
Neighborhood of ATM
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
An autosomal recessive inherited disorder characterized by choreoathetosis beginning in childhood, progressive CEREBELLAR ATAXIA; TELANGIECTASIS of CONJUNCTIVA and SKIN; DYSARTHRIA; B- and T-cell immunodeficiency, and RADIOSENSITIVITY to IONIZING RADIATION. Affected individuals are prone to recurrent sinobronchopulmonary infections, lymphoreticular neoplasms, and other malignancies. Serum ALPHA-FETOPROTEINS are usually elevated. (Menkes, Textbook of Child Neurology, 5th ed, p688) The gene for this disorder (ATM) encodes a cell cycle checkpoint protein kinase and has been mapped to chromosome 11 (11q22-q23).
Generated by gene2mesh v. 1.1.1
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 Melanoma. The EFO term melanoma 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:
JH Barrett, MM Iles, M Harland, JC Taylor, JF Aitken, PA Andresen, LA Akslen, BK Armstrong, MF Avril, E Azizi, B Bakker, W Bergman, G Bianchi-Scarrà , B Bressac-de Paillerets, D Calista, LA Cannon-Albright, E Corda, AE Cust, T Dębniak, D Duffy, AM Dunning, DF Easton, E Friedman, P Galan, P Ghiorzo, GG Giles, J Hansson, M Hocevar, V Höiom, JL Hopper, C Ingvar, B Janssen, MA Jenkins, G Jönsson, RF Kefford, G Landi, MT Landi, J Lang, J Lubiński, R Mackie, J Malvehy, NG Martin, A Molven, GW Montgomery, FA van Nieuwpoort, S Novakovic, H Olsson, L Pastorino, S Puig, JA Puig-Butille, J Randerson-Moor, H Snowden, R Tuominen, P Van Belle, N van der Stoep, DC Whiteman, D Zelenika, J Han, S Fang, JE Lee, Q Wei, GM Lathrop, EM Gillanders, KM Brown, AM Goldstein, PA Kanetsky, GJ Mann, S Macgregor, DE Elder, CI Amos, NK Hayward, NA Gruis, F Demenais, JA Bishop, DT Bishop
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "SAGA complex", which is defined as "A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8." 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 "SAGA complex", which is defined as "A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8." 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
When transfected into MDA-MB-231 and BT-549 breast cancer cells mir-302b confers cisplatin-sensitivity. HGNC identifer was assigned manually. Therapy:Cisplatin. Response Type:Sensitive
Authors:
Cataldo A, Cheung DG, Balsari A, Tagliabue E, Coppola V, Iorio MV, Palmieri D, Croce CM
When transfected into T47D breast cancer cells mir-302b confers cisplatin-sensitivity. HGNC identifer was assigned manually. Therapy:Cisplatin. Response Type:Sensitive
Authors:
Cataldo A, Cheung DG, Balsari A, Tagliabue E, Coppola V, Iorio MV, Palmieri D, Croce CM
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.
Whole Brain Gene Expression Correlates for ACTI15_SAL measured in BXD RI Females obtained using INIA Brain mRNA M430 (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
Neocortex Gene Expression Correlates for ST_PCT_PPI_85 measured in BXD RI Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The ST_PCT_PPI_85 measures Prepulse inhibition at 85db 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 ST_PCT_STARTLE_85 measured in BXD RI Males obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The ST_PCT_STARTLE_85 measures Acoustic Startle Response Percentage of maximum response at 85 db 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
These genes are a 1 class SAM significant (1% FDR) in nucleus accumbens (core + shell) for saline treated ("basal") control vs. Fyn KO mice. The list was filtered for an average Sscore >2.0 or <-2.0. Data from Farris and Miles, PLoS One, 2013.
cocaine related behavior 8 (Cocrb8) spans 26.931283 - 76.931283 Mbp (NCBI Build 37) on Chr 9. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
cocaine related behavior 9 (Cocrb9) spans 49.746096 - 99.746096 Mbp (NCBI Build 37) on Chr 9. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
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