This gene set shows considerable overlap with genes that are disrupted by single de novo CNVs in children with ASD. There is potential that these de novo SNVs are indicative of the major effect locus responsible for ASD-associated features.
Authors:
Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Beau Reilly, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Raphael Bernier, Jay Shendure & Evan E. Eichler
21 non-synonymous de novo mutations were mapped in a CNV region that is often recognized in children who display developmental delay and ASD.
Authors:
Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Beau Reilly, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Raphael Bernier, Jay Shendure & Evan E. Eichler
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 Drug-induced torsades de pointes. The EFO term torsades de pointes, response to drug 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:
ER Behr, MD Ritchie, T Tanaka, S Kääb, DC Crawford, P Nicoletti, A Floratos, MF Sinner, PJ Kannankeril, AA Wilde, CR Bezzina, E Schulze-Bahr, S Zumhagen, P Guicheney, NH Bishopric, V Marshall, S Shakir, C Dalageorgou, S Bevan, Y Jamshidi, R Bastiaenen, RJ Myerburg, JJ Schott, AJ Camm, G Steinbeck, K Norris, RB Altman, NP Tatonetti, S Jeffery, M Kubo, Y Nakamura, Y Shen, AL George, DM Roden
ASD probands were scanned for rare inherited CNVs or de novo CNVs where 76 events were found from 53 individuals. Such events included disruptions in particular genes that involved in development and/or associated with bipolar disorder and schizophrenia.
Authors:
Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Beau Reilly, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Raphael Bernier, Jay Shendure & Evan E. Eichler
Human Phenotype Ontology (HPO) gene set. This set contains genes that have been annotated to the HPO term "Autosomal dominant germline de novo mutation", which is defined as "Being related to a mutation that gamete that participates in fertilization. All cells of the emerging organism will be affected and the variant canl be passed on to the next generation." This gene set was automatically constructed using annotation and ontology data provided by HPO and includes gene-phenotypes annotations from all HPO sources. The transitive closure of this term is taken into account using is_a relationships. For more information: The Human Phenotype Ontology Consortium (HPOC), http://human-phenotype-ontology.org This gene set was generated using the GeneWeaver HPO loader v. 0.1.5, HPO OBO v. hp/releases/2020-03-27, and HPO Genes to Phenotypes (all sources, all frequencies) v. 2020.05.06.
Authors:
S Köhler, SC Doelken, CJ Mungall, S Bauer, HV Firth, I Bailleul-Forestier, GC Black, DL Brown, M Brudno, J Campbell, DR FitzPatrick, JT Eppig, AP Jackson, K Freson, M Girdea, I Helbig, JA Hurst, J Jähn, LG Jackson, AM Kelly, DH Ledbetter, S Mansour, CL Martin, C Moss, A Mumford, WH Ouwehand, SM Park, ER Riggs, RH Scott, S Sisodiya, S Van Vooren, RJ Wapner, AO Wilkie, CF Wright, AT Vulto-van Silfhout, N de Leeuw, BB de Vries, NL Washingthon, CL Smith, M Westerfield, P Schofield, BJ Ruef, GV Gkoutos, M Haendel, D Smedley, SE Lewis, PN Robinson
Human Phenotype Ontology (HPO) gene set. This set contains genes that have been annotated to the HPO term "Torsade de pointes", which is defined as "A type of ventricular tachycardia characterized by polymorphioc QRS complexes that change in amplitue and cycle length, and thus have the appearance of oscillating around the baseline in the EKG." This gene set was automatically constructed using annotation and ontology data provided by HPO and includes gene-phenotypes annotations from all HPO sources. The transitive closure of this term is taken into account using is_a relationships. For more information: The Human Phenotype Ontology Consortium (HPOC), http://human-phenotype-ontology.org This gene set was generated using the GeneWeaver HPO loader v. 0.1.5, HPO OBO v. hp/releases/2020-03-27, and HPO Genes to Phenotypes (all sources, all frequencies) v. 2020.05.06.
Authors:
S Köhler, SC Doelken, CJ Mungall, S Bauer, HV Firth, I Bailleul-Forestier, GC Black, DL Brown, M Brudno, J Campbell, DR FitzPatrick, JT Eppig, AP Jackson, K Freson, M Girdea, I Helbig, JA Hurst, J Jähn, LG Jackson, AM Kelly, DH Ledbetter, S Mansour, CL Martin, C Moss, A Mumford, WH Ouwehand, SM Park, ER Riggs, RH Scott, S Sisodiya, S Van Vooren, RJ Wapner, AO Wilkie, CF Wright, AT Vulto-van Silfhout, N de Leeuw, BB de Vries, NL Washingthon, CL Smith, M Westerfield, P Schofield, BJ Ruef, GV Gkoutos, M Haendel, D Smedley, SE Lewis, PN Robinson
Sets of genes within a 1-5% coding exon territory that were suspected to be involved in autism risk were analyzed to determine if there was a significant enhancement for de novo mutations.
Authors:
Benjamin M. Neale, Yan Kou, Li Liu, Avi Ma’ayan, Kaitlin E. Samocha, Aniko Sabo, Chiao-Feng Lin, Christine Stevens, Li-San Wang, Vladimir Makarov, Paz Polak, Seungtai Yoon, Jared Maguire, Emily L. Crawford, Nicholas G. Campbell, Evan T. Geller, Otto Valladares, Chad Schafer, Han Liu, Tuo Zhao, Guiqing Cai, Jayon Lihm, Ruth Dannenfelser, Omar Jabado, Zuleyma Peralta, Uma Nagaswamy, Donna Muzny, Jeffrey G. Reid, Irene Newsham, Yuanqing Wu, Lora Lewis, Yi Han, Benjamin F. Voight, Elaine Lim, Elizabeth Rossin, Andrew Kirby, Jason Flannick, Menachem Fromer, Khalid Shakir, Tim Fennell, Kiran Garimella, Eric Banks, Ryan Poplin, Stacey Gabriel, Mark DePristo, Jack R. Wimbish, Braden E. Boone, Shawn E. Levy, Catalina Betancur, Shamil Sunyaev, Eric Boerwinkle, Joseph D. Buxbaum, Edwin H. Cook Jr, Bernie Devlin, Richard A. Gibbs, Kathryn Roeder, Gerard D. Schellenberg, James S. Sutcliffe & Mark J. Daly
Exomes were sequenced in parent-child autism trios to determine if de novo mutations are responsible for risk of developing ASD in families with no prior history.
Authors:
Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Beau Reilly, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Raphael Bernier, Jay Shendure & Evan E. Eichler
Genes associated with nan that interact with the MeSH term 'angiotensin II, des-Asp(1)-des-Arg(2)-Ile(5)-' (C012877). 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 Homo sapiens that interact with the MeSH term 'kallidin, des-Arg(10)-' (C052787). Incorporates data from 3 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with nan that interact with the MeSH term 'bradykinin, des-Arg(9)-' (C024626). Incorporates data from 10 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
QTL Associated with epididymal fat pad mass. On Chromosome 8 with a LOD score= 11.78, p-value =0.001. From a(n) intercross of QTL Associated with Consumption level. On Chromosome 9 with a LOD score= 9.8, p-value =0.001. From a(n) intercross of
Authors:
Marissal-Arvy N, Diane A, Moisan MP, Larue-Achagiotis C, Tridon C, Tome D, Fromentin G, Mormède P
Online Mendelian Inheritance in Man (OMIM) Geneset. This geneset contains genes that have been mapped to the following disorder: Cornelia de Lange syndrome 4. This data was retrieved and parsed from the Morbid Map dataset provided by OMIM.
gene2omim v. 0.1.0
Last updated 2015.08.31
Online Mendelian Inheritance in Man (OMIM) Geneset. This geneset contains genes that have been mapped to the following disorder: De la Chapelle dysplasia. This data was retrieved and parsed from the Morbid Map dataset provided by OMIM.
gene2omim v. 0.1.0
Last updated 2015.08.31
Online Mendelian Inheritance in Man (OMIM) Geneset. This geneset contains genes that have been mapped to the following disorder: De Sanctis-Cacchione syndrome. This data was retrieved and parsed from the Morbid Map dataset provided by OMIM.
gene2omim v. 0.1.0
Last updated 2015.08.31
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "tetrahydrobiopterin de novo biosynthesis" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is HumanCyc.
gene2pc v. 0.1.0
Last updated 2015.08.31
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "purine nucleotides de novo biosynthesis" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is HumanCyc.
gene2pc v. 0.1.0
Last updated 2015.08.31
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "guanosine ribonucleotides de novo biosynthesis" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is HumanCyc.
gene2pc v. 0.1.0
Last updated 2015.08.31
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "NAD de novo biosynthesis" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is HumanCyc.
gene2pc v. 0.1.0
Last updated 2015.08.31
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "De novo pyrimidine ribonucleotides biosythesis" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is PANTHER.
gene2pc v. 0.1.0
Last updated 2015.08.31
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "ornithine de novo biosynthesis" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is HumanCyc.
gene2pc v. 0.1.0
Last updated 2015.08.31
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis
Description:
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is HumanCyc.
gene2pc v. 0.1.0
Last updated 2015.08.31
pyrimidine deoxyribonucleotides de novo biosynthesis
Description:
Pathway Commons (PC) Geneset. This geneset contains genes that participate in the "pyrimidine deoxyribonucleotides de novo biosynthesis" pathway. This set was automatically constructed using the PC API.
The original source of this geneset is HumanCyc.
gene2pc v. 0.1.0
Last updated 2015.08.31
GeneWeaver