Literature DB >> 27070863

The statistical properties of gene-set analysis.

Christiaan A de Leeuw1,2, Benjamin M Neale3,4, Tom Heskes2, Danielle Posthuma1,5.   

Abstract

The rapid increase in loci discovered in genome-wide association studies has created a need to understand the biological implications of these results. Gene-set analysis provides a means of gaining such understanding, but the statistical properties of gene-set analysis are not well understood, which compromises our ability to interpret its results. In this Analysis article, we provide an extensive statistical evaluation of the core structure that is inherent to all gene- set analyses and we examine current implementations in available tools. We show which factors affect valid and successful detection of gene sets and which provide a solid foundation for performing and interpreting gene-set analysis.

Mesh：

Year:  2016        PMID： 27070863     DOI： 10.1038/nrg.2016.29

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  41 in total

Review 1.  Analysing biological pathways in genome-wide association studies.

Authors:  Kai Wang; Mingyao Li; Hakon Hakonarson
Journal:  Nat Rev Genet       Date:  2010-12       Impact factor: 53.242

Review 2.  Functional and genomic context in pathway analysis of GWAS data.

Authors:  Michael A Mooney; Joel T Nigg; Shannon K McWeeney; Beth Wilmot
Journal:  Trends Genet       Date:  2014-08-22       Impact factor: 11.639

3.  Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder.

Authors:  Peter Holmans; Elaine K Green; Jaspreet Singh Pahwa; Manuel A R Ferreira; Shaun M Purcell; Pamela Sklar; Michael J Owen; Michael C O'Donovan; Nick Craddock
Journal:  Am J Hum Genet       Date:  2009-06-18       Impact factor: 11.025

Review 4.  Gene set analysis of genome-wide association studies: methodological issues and perspectives.

Authors:  Lily Wang; Peilin Jia; Russell D Wolfinger; Xi Chen; Zhongming Zhao
Journal:  Genomics       Date:  2011-04-30       Impact factor: 5.736

5.  Genome-wide association study identifies five new schizophrenia loci.

Authors: 
Journal:  Nat Genet       Date:  2011-09-18       Impact factor: 38.330

6.  Biological interpretation of genome-wide association studies using predicted gene functions.

Authors:  Tune H Pers; Juha M Karjalainen; Yingleong Chan; Harm-Jan Westra; Andrew R Wood; Jian Yang; Julian C Lui; Sailaja Vedantam; Stefan Gustafsson; Tonu Esko; Tim Frayling; Elizabeth K Speliotes; Michael Boehnke; Soumya Raychaudhuri; Rudolf S N Fehrmann; Joel N Hirschhorn; Lude Franke
Journal:  Nat Commun       Date:  2015-01-19       Impact factor: 14.919

7.  Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn's Disease dataset.

Authors:  Hongsheng Gui; Miaoxin Li; Pak C Sham; Stacey S Cherny
Journal:  BMC Res Notes       Date:  2011-10-07

8.  The Reactome pathway knowledgebase.

Authors:  David Croft; Antonio Fabregat Mundo; Robin Haw; Marija Milacic; Joel Weiser; Guanming Wu; Michael Caudy; Phani Garapati; Marc Gillespie; Maulik R Kamdar; Bijay Jassal; Steven Jupe; Lisa Matthews; Bruce May; Stanislav Palatnik; Karen Rothfels; Veronica Shamovsky; Heeyeon Song; Mark Williams; Ewan Birney; Henning Hermjakob; Lincoln Stein; Peter D'Eustachio
Journal:  Nucleic Acids Res       Date:  2013-11-15       Impact factor: 16.971

9.  Genome-wide association analysis identifies 13 new risk loci for schizophrenia.

Authors:  Stephan Ripke; Colm O'Dushlaine; Kimberly Chambert; Jennifer L Moran; Anna K Kähler; Susanne Akterin; Sarah E Bergen; Ann L Collins; James J Crowley; Menachem Fromer; Yunjung Kim; Sang Hong Lee; Patrik K E Magnusson; Nick Sanchez; Eli A Stahl; Stephanie Williams; Naomi R Wray; Kai Xia; Francesco Bettella; Anders D Borglum; Brendan K Bulik-Sullivan; Paul Cormican; Nick Craddock; Christiaan de Leeuw; Naser Durmishi; Michael Gill; Vera Golimbet; Marian L Hamshere; Peter Holmans; David M Hougaard; Kenneth S Kendler; Kuang Lin; Derek W Morris; Ole Mors; Preben B Mortensen; Benjamin M Neale; Francis A O'Neill; Michael J Owen; Milica Pejovic Milovancevic; Danielle Posthuma; John Powell; Alexander L Richards; Brien P Riley; Douglas Ruderfer; Dan Rujescu; Engilbert Sigurdsson; Teimuraz Silagadze; August B Smit; Hreinn Stefansson; Stacy Steinberg; Jaana Suvisaari; Sarah Tosato; Matthijs Verhage; James T Walters; Douglas F Levinson; Pablo V Gejman; Kenneth S Kendler; Claudine Laurent; Bryan J Mowry; Michael C O'Donovan; Michael J Owen; Ann E Pulver; Brien P Riley; Sibylle G Schwab; Dieter B Wildenauer; Frank Dudbridge; Peter Holmans; Jianxin Shi; Margot Albus; Madeline Alexander; Dominique Campion; David Cohen; Dimitris Dikeos; Jubao Duan; Peter Eichhammer; Stephanie Godard; Mark Hansen; F Bernard Lerer; Kung-Yee Liang; Wolfgang Maier; Jacques Mallet; Deborah A Nertney; Gerald Nestadt; Nadine Norton; Francis A O'Neill; George N Papadimitriou; Robert Ribble; Alan R Sanders; Jeremy M Silverman; Dermot Walsh; Nigel M Williams; Brandon Wormley; Maria J Arranz; Steven Bakker; Stephan Bender; Elvira Bramon; David Collier; Benedicto Crespo-Facorro; Jeremy Hall; Conrad Iyegbe; Assen Jablensky; Rene S Kahn; Luba Kalaydjieva; Stephen Lawrie; Cathryn M Lewis; Kuang Lin; Don H Linszen; Ignacio Mata; Andrew McIntosh; Robin M Murray; Roel A Ophoff; John Powell; Dan Rujescu; Jim Van Os; Muriel Walshe; Matthias Weisbrod; Durk Wiersma; Peter Donnelly; Ines Barroso; Jenefer M Blackwell; Elvira Bramon; Matthew A Brown; Juan P Casas; Aiden P Corvin; Panos Deloukas; Audrey Duncanson; Janusz Jankowski; Hugh S Markus; Christopher G Mathew; Colin N A Palmer; Robert Plomin; Anna Rautanen; Stephen J Sawcer; Richard C Trembath; Ananth C Viswanathan; Nicholas W Wood; Chris C A Spencer; Gavin Band; Céline Bellenguez; Colin Freeman; Garrett Hellenthal; Eleni Giannoulatou; Matti Pirinen; Richard D Pearson; Amy Strange; Zhan Su; Damjan Vukcevic; Peter Donnelly; Cordelia Langford; Sarah E Hunt; Sarah Edkins; Rhian Gwilliam; Hannah Blackburn; Suzannah J Bumpstead; Serge Dronov; Matthew Gillman; Emma Gray; Naomi Hammond; Alagurevathi Jayakumar; Owen T McCann; Jennifer Liddle; Simon C Potter; Radhi Ravindrarajah; Michelle Ricketts; Avazeh Tashakkori-Ghanbaria; Matthew J Waller; Paul Weston; Sara Widaa; Pamela Whittaker; Ines Barroso; Panos Deloukas; Christopher G Mathew; Jenefer M Blackwell; Matthew A Brown; Aiden P Corvin; Mark I McCarthy; Chris C A Spencer; Elvira Bramon; Aiden P Corvin; Michael C O'Donovan; Kari Stefansson; Edward Scolnick; Shaun Purcell; Steven A McCarroll; Pamela Sklar; Christina M Hultman; Patrick F Sullivan
Journal:  Nat Genet       Date:  2013-08-25       Impact factor: 38.330

10.  Biological insights from 108 schizophrenia-associated genetic loci.

Authors: 
Journal:  Nature       Date:  2014-07-22       Impact factor: 49.962
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  88 in total

Review 1.  Beyond genome-wide significance: integrative approaches to the interpretation and extension of GWAS findings for alcohol use disorder.

Authors:  Jessica E Salvatore; Shizhong Han; Sean P Farris; Kristin M Mignogna; Michael F Miles; Arpana Agrawal
Journal:  Addict Biol       Date:  2018-01-09       Impact factor: 4.280

2.  Sharing of Genes and Pathways Across Complex Phenotypes: A Multilevel Genome-Wide Analysis.

Authors:  Hongsheng Gui; Johnny S Kwan; Pak C Sham; Stacey S Cherny; Miaoxin Li
Journal:  Genetics       Date:  2017-05-11       Impact factor: 4.562

3.  Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression.

Authors:  Mads Engel Hauberg; Wen Zhang; Claudia Giambartolomei; Oscar Franzén; David L Morris; Timothy J Vyse; Arno Ruusalepp; Pamela Sklar; Eric E Schadt; Johan L M Björkegren; Panos Roussos
Journal:  Am J Hum Genet       Date:  2017-05-25       Impact factor: 11.025

4.  Application of the parametric bootstrap for gene-set analysis of gene-environment interactions.

Authors:  Brandon J Coombes; Joanna M Biernacka
Journal:  Eur J Hum Genet       Date:  2018-08-08       Impact factor: 4.246

5.  Gene-set analysis shows association between FMRP targets and autism spectrum disorder.

Authors:  Arija Jansen; Gwen C Dieleman; August B Smit; Matthijs Verhage; Frank C Verhulst; Tinca J C Polderman; Danielle Posthuma
Journal:  Eur J Hum Genet       Date:  2017-04-19       Impact factor: 4.246

6.  Analysis of genome-wide association data highlights candidates for drug repositioning in psychiatry.

Authors:  Hon-Cheong So; Carlos Kwan-Long Chau; Wan-To Chiu; Kin-Sang Ho; Cho-Pong Lo; Stephanie Ho-Yue Yim; Pak-Chung Sham
Journal:  Nat Neurosci       Date:  2017-08-14       Impact factor: 24.884

7.  IMPROVED PERFORMANCE OF GENE SET ANALYSIS ON GENOME-WIDE TRANSCRIPTOMICS DATA WHEN USING GENE ACTIVITY STATE ESTIMATES.

Authors:  Thomas Kamp; Micah Adams; Craig Disselkoen; Nathan Tintle
Journal:  Pac Symp Biocomput       Date:  2017

Review 8.  Advancing the use of genome-wide association studies for drug repurposing.

Authors:  William R Reay; Murray J Cairns
Journal:  Nat Rev Genet       Date:  2021-07-23       Impact factor: 53.242

9.  No Evidence That Schizophrenia Candidate Genes Are More Associated With Schizophrenia Than Noncandidate Genes.

Authors:  Emma C Johnson; Richard Border; Whitney E Melroy-Greif; Christiaan A de Leeuw; Marissa A Ehringer; Matthew C Keller
Journal:  Biol Psychiatry       Date:  2017-07-13       Impact factor: 13.382

10.  Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways.

Authors:  Xu Chi; Maureen A Sartor; Sanghoon Lee; Meenakshi Anurag; Snehal Patil; Pelle Hall; Matthew Wexler; Xiao-Song Wang
Journal:  Brief Bioinform       Date:  2020-09-25       Impact factor: 11.622
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