Multiple sources of bias confound functional enrichment analysis of global -omics data

Genome Biology
James A TimmonsIain J Gallagher

Abstract

Serious and underappreciated sources of bias mean that extreme caution should be applied when using or interpreting functional enrichment analysis to validate findings from global RNA- or protein-expression analyses.

References

Dec 19, 2003·Nucleic Acids Research·M A HarrisUNKNOWN Gene Ontology Consortium
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Aug 27, 2010·American Journal of Physiology. Endocrinology and Metabolism·A C AlibegovicA Vaag
Oct 12, 2010·Journal of Applied Physiology·Pernille KellerJames A Timmons
Jul 13, 2011·Nature Biotechnology·Kasper D HansenJeffrey T Leek
Nov 5, 2011·Journal of Proteome Research·Sidney B CambridgeMatthias Mann
Apr 9, 2014·Cell Metabolism·Jonathan Z LongBruce M Spiegelman
Jul 13, 2014·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Malene E LindholmCarl J Sundberg
Oct 15, 2014·Proceedings of the National Academy of Sciences of the United States of America·Steve HorvathJochen Hampe

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Citations

Apr 21, 2016·Nucleic Acids Research·Sanjana SoodJames A Timmons
Sep 20, 2016·Journal of Psychiatric Research·Charlotte A M CecilEssi Viding
Nov 5, 2016·Nature Reviews. Rheumatology·Kwangwoo KimSang-Cheol Bae
Feb 25, 2017·BMC Genomics·Benoit LaurentMarie Foulongne-Oriol
Aug 5, 2016·The American Journal of Clinical Nutrition·Asif NakhudaJames A Timmons
Jul 30, 2017·Physiological Genomics·Galina Y ZheleznyakovaLara Kular
Sep 28, 2017·American Journal of Respiratory and Critical Care Medicine·Brian D Modena
Jul 10, 2018·Nucleic Acids Research·James A TimmonsWilliam E Kraus
Sep 6, 2018·Physiological Reviews·Markus M RinschenTrairak Pisitkun
Aug 24, 2018·Proteomics. Clinical Applications·Klaus Kratochwill
Jun 16, 2016·F1000Research·James A Timmons, Iain J Gallagher
Dec 24, 2018·Molecular Systems Biology·Evan A BoyleWilliam J Greenleaf
Jun 7, 2019·Aging Cell·James A TimmonsClaes Wahlestedt
Jan 3, 2018·Psychiatry and Clinical Neurosciences·Lara Kular, Sonia Kular
Jan 14, 2020·Genome Génome / Conseil National De Recherches Canada·Yuanlang WangYueyun Ding
Sep 5, 2019·PloS One·Linden J GearingPaul J Hertzog
Jul 12, 2019·PLoS Computational Biology·Guido ZampieriClaudio Angione
Apr 11, 2019·Frontiers in Physiology·Fakhreddin Yaghoob NezhadHenning Wackerhage
Oct 28, 2019·Frontiers in Genetics·Gillian P McHugoDavid E MacHugh
Dec 13, 2019·Frontiers in Genetics·Anna Bogucka-KockaJanusz Kocki
Jun 6, 2020·Frontiers in Psychiatry·Maria Salud García-GutiérrezJorge Manzanares
Aug 1, 2020·Frontiers in Genetics·Jian-Tao ZhengHong-Dong Li
Mar 10, 2018·Frontiers in Genetics·Sam BrowettDavid E MacHugh
Mar 11, 2020·Scientific Reports·Evans KatakaDmitrij Frishman
Sep 21, 2020·Proteomics·Johanna TüshausStefan F Lichtenthaler
Mar 25, 2020·Computational and Structural Biotechnology Journal·Lucile Broseus, William Ritchie
Jan 21, 2021·International Journal of Molecular Sciences·Daniela LaricchiutaLaura Petrosini

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Methods Mentioned

BETA
chip
biopsy
RNA-seq

Software Mentioned

DAVID
DAVID Database for Annotation Visualization Integrated Discovery
IPA
Ingenuity

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