Literature DB >> 35474380

ExPheWas: a platform for cis-Mendelian randomization and gene-based association scans.

Marc-André Legault1,2,3, Louis-Philippe Lemieux Perreault1,2, Jean-Claude Tardif1,4, Marie-Pierre Dubé1,2,4.   

Abstract

Establishing the relationship between protein-coding genes and phenotypes has the potential to inform on the molecular etiology of diseases. Here, we describe ExPheWas (exphewas.ca), a gene-based phenome-wide association study browser and platform that enables the conduct of gene-based Mendelian randomization. The ExPheWas data repository includes sex-stratified and sex-combined gene-based association results from 26 616 genes with 1746 phenotypes measured in up to 413 133 individuals from the UK Biobank. Interactive visualizations are provided through a browser to facilitate data exploration supported by false discovery rate control, and it includes tools for enrichment analysis. The interactive Mendelian randomization module in ExPheWas allows the estimation of causal effects of a genetically predicted exposure on an outcome by using genetic variation in a single gene as the instrumental variable.
© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2022        PMID： 35474380      PMCID： PMC9252780          DOI： 10.1093/nar/gkac289

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   19.160


  25 in total

1.  A versatile gene-based test for genome-wide association studies.

Authors:  Jimmy Z Liu; Allan F McRae; Dale R Nyholt; Sarah E Medland; Naomi R Wray; Kevin M Brown; Nicholas K Hayward; Grant W Montgomery; Peter M Visscher; Nicholas G Martin; Stuart Macgregor
Journal:  Am J Hum Genet       Date:  2010-07-09       Impact factor: 11.025

2.  Gene-based association tests using GWAS summary statistics.

Authors:  Gulnara R Svishcheva; Nadezhda M Belonogova; Irina V Zorkoltseva; Anatoly V Kirichenko; Tatiana I Axenovich
Journal:  Bioinformatics       Date:  2019-10-01       Impact factor: 6.937

3.  Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.

Authors:  Maya Ghoussaini; Edward Mountjoy; Miguel Carmona; Gareth Peat; Ellen M Schmidt; Andrew Hercules; Luca Fumis; Alfredo Miranda; Denise Carvalho-Silva; Annalisa Buniello; Tony Burdett; James Hayhurst; Jarrod Baker; Javier Ferrer; Asier Gonzalez-Uriarte; Simon Jupp; Mohd Anisul Karim; Gautier Koscielny; Sandra Machlitt-Northen; Cinzia Malangone; Zoe May Pendlington; Paola Roncaglia; Daniel Suveges; Daniel Wright; Olga Vrousgou; Eliseo Papa; Helen Parkinson; Jacqueline A L MacArthur; John A Todd; Jeffrey C Barrett; Jeremy Schwartzentruber; David G Hulcoop; David Ochoa; Ellen M McDonagh; Ian Dunham
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

4.  PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.

Authors:  Joshua C Denny; Marylyn D Ritchie; Melissa A Basford; Jill M Pulley; Lisa Bastarache; Kristin Brown-Gentry; Deede Wang; Dan R Masys; Dan M Roden; Dana C Crawford
Journal:  Bioinformatics       Date:  2010-03-24       Impact factor: 6.937

5.  Testing association between disease and multiple SNPs in a candidate gene.

Authors:  W James Gauderman; Cassandra Murcray; Frank Gilliland; David V Conti
Journal:  Genet Epidemiol       Date:  2007-07       Impact factor: 2.135

6.  Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data.

Authors:  Joshua C Denny; Lisa Bastarache; Marylyn D Ritchie; Robert J Carroll; Raquel Zink; Jonathan D Mosley; Julie R Field; Jill M Pulley; Andrea H Ramirez; Erica Bowton; Melissa A Basford; David S Carrell; Peggy L Peissig; Abel N Kho; Jennifer A Pacheco; Luke V Rasmussen; David R Crosslin; Paul K Crane; Jyotishman Pathak; Suzette J Bielinski; Sarah A Pendergrass; Hua Xu; Lucia A Hindorff; Rongling Li; Teri A Manolio; Christopher G Chute; Rex L Chisholm; Eric B Larson; Gail P Jarvik; Murray H Brilliant; Catherine A McCarty; Iftikhar J Kullo; Jonathan L Haines; Dana C Crawford; Daniel R Masys; Dan M Roden
Journal:  Nat Biotechnol       Date:  2013-12       Impact factor: 54.908

7.  Mendelian randomization analysis with multiple genetic variants using summarized data.

Authors:  Stephen Burgess; Adam Butterworth; Simon G Thompson
Journal:  Genet Epidemiol       Date:  2013-09-20       Impact factor: 2.135

8.  MAGMA: generalized gene-set analysis of GWAS data.

Authors:  Christiaan A de Leeuw; Joris M Mooij; Tom Heskes; Danielle Posthuma
Journal:  PLoS Comput Biol       Date:  2015-04-17       Impact factor: 4.475

9.  g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).

Authors:  Uku Raudvere; Liis Kolberg; Ivan Kuzmin; Tambet Arak; Priit Adler; Hedi Peterson; Jaak Vilo
Journal:  Nucleic Acids Res       Date:  2019-07-02       Impact factor: 16.971

10.  The UK Biobank resource with deep phenotyping and genomic data.

Authors:  Clare Bycroft; Colin Freeman; Desislava Petkova; Gavin Band; Lloyd T Elliott; Kevin Sharp; Allan Motyer; Damjan Vukcevic; Olivier Delaneau; Jared O'Connell; Adrian Cortes; Samantha Welsh; Alan Young; Mark Effingham; Gil McVean; Stephen Leslie; Naomi Allen; Peter Donnelly; Jonathan Marchini
Journal:  Nature       Date:  2018-10-10       Impact factor: 49.962
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