Towards Consensus Gene Ages

Genome Biology and Evolution
Benjamin J LiebeskindEdward M Marcotte

Abstract

Correctly estimating the age of a gene or gene family is important for a variety of fields, including molecular evolution, comparative genomics, and phylogenetics, and increasingly for systems biology and disease genetics. However, most studies use only a point estimate of a gene's age, neglecting the substantial uncertainty involved in this estimation. Here, we characterize this uncertainty by investigating the effect of algorithm choice on gene-age inference and calculate consensus gene ages with attendant error distributions for a variety of model eukaryotes. We use 13 orthology inference algorithms to create gene-age datasets and then characterize the error around each age-call on a per-gene and per-algorithm basis. Systematic error was found to be a large factor in estimating gene age, suggesting that simple consensus algorithms are not enough to give a reliable point estimate. We also found that different sources of error can affect downstream analyses, such as gene ontology enrichment. Our consensus gene-age datasets, with associated error terms, are made fully available at so that researchers can propagate this uncertainty through their analyses (geneages.org).

References

Mar 10, 2017·Journal of Bioinformatics and Computational Biology·Masih Sherafatian, Seyed Javad Mowla
Apr 13, 2017·Genome Research·José M Martín-DuránAndreas Hejnol
Aug 8, 2017·Molecular BioSystems·Sanghita Banerjee, Sandip Chakraborty
Jan 18, 2018·Medicinal Research Reviews·Yuan QuanHong-Yu Zhang
Nov 1, 2018·Nucleic Acids Research·Yannis NeversOdile Lecompte
Jan 17, 2019·Genome Biology and Evolution·Arpit JainIngo Ebersberger
Apr 27, 2019·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Jolien J E van HooffBerend Snel
Mar 16, 2019·Bioinformatics·Zebulun ArendseeEve Syrkin Wurtele
Jun 27, 2019·Molecular Biology and Evolution·Natasha GloverPaul D Thomas
Aug 1, 2020·Biomolecules·Mátyás PajkosZsuzsanna Dosztányi
Jul 11, 2019·Journal of Bioinformatics and Computational Biology·Chun-Yu LinTatsuya Akutsu
Feb 20, 2019·BMC Bioinformatics·Xiong-Hui ZhouHong-Yu Zhang

Citations

Jun 1, 1970·Systematic Zoology·W M Fitch
Sep 17, 1996·Proceedings of the National Academy of Sciences of the United States of America·A R Mushegian, Eugene V Koonin
Jan 27, 1999·Bioinformatics·S R Eddy
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·M PellegriniT O Yeates
Apr 27, 2000·Trends in Genetics : TIG·W M Fitch
May 9, 2006·Bioinformatics·Marc A Suchard, Benjamin D Redelings
Oct 27, 2007·Nucleic Acids Research·Jaime Huerta-CepasToni Gabaldón
Sep 30, 2008·Molecular Biology and Evolution·Tomislav Domazet-Loso, Diethard Tautz
Nov 6, 2008·Genome Biology·Toni Gabaldón
Nov 26, 2008·Genome Research·Albert J VilellaEwan Birney
Apr 9, 2009·Proceedings of the National Academy of Sciences of the United States of America·Yuri I WolfDavid J Lipman
Apr 28, 2010·Bioinformatics·Jeet Sukumaran, Mark T Holder
Jan 17, 2012·Bioinformatics·Todd DeLucaDennis P Wall
Jun 23, 2012·Proceedings of the National Academy of Sciences of the United States of America·Cecilia ConacoKenneth S Kosik
Apr 5, 2013·Nature Reviews. Genetics·Toni Gabaldón, Eugene V Koonin
Jul 31, 2013·Critical Reviews in Biochemistry and Molecular Biology·V Lila KoumandouMark C Field
Aug 7, 2013·Trends in Genetics : TIG·John A CapraKatherine S Pollard
May 2, 2014·Molecular Biology and Evolution·Ammon ThompsonHarold H Zakon
Jul 30, 2014·Bioinformatics·Erik SonnhammerQuest for Orthologs consortium
Oct 3, 2014·Bioinformatics·Benjamin LinardOdile Lecompte
Oct 15, 2014·Molecular Biology and Evolution·Bryan A Moyers, Jianzhi Zhang
Nov 29, 2014·Nucleic Acids Research·Erik Sonnhammer, Gabriel Östlund
Jan 15, 2015·Genome Biology·Brian Tjaden
Jan 21, 2015·Trends in Ecology & Evolution·Raphaël MéheustEric Bapteste
Jul 2, 2015·Systematic Biology·Ikram UllahJens Lagergren
Jul 3, 2015·Genome Biology and Evolution·Brigitte BoeckmannQuest for Orthologs Species Tree Working Group
Sep 8, 2015·Nature·Cuihong WanAndrew Emili
Dec 9, 2015·Proceedings of the National Academy of Sciences of the United States of America·Alexandre AliéNoriko Funayama
Jan 10, 2016·Trends in Ecology & Evolution·Benjamin J LiebeskindHans A Hofmann
Jan 14, 2016·Molecular Biology and Evolution·Bryan A Moyers, Jianzhi Zhang
Jan 19, 2016·Trends in Ecology & Evolution·August GuangCasey W Dunn
Feb 4, 2016·Nature·Alexandros A Pittis, Toni Gabaldón
Apr 5, 2016·Nature Methods·Adrian M AltenhoffChristophe Dessimoz

Related Concepts

Genes
Genes, Reiterated
Infarction, Anterior Cerebral Artery
Research Personnel
Phylogeny
Gene Delivery Systems
Genomics
Comparative Genomic Analysis
Genes, vif
Cistron

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Sexual Dimorphism in Neurodegeneration

There exist sex differences in neurodevelopmental and neurodegenerative disorders. For instance, multiple sclerosis is more common in women, whereas Parkinson’s disease is more common in men. Here is the latest research on sexual dimorphism in neurodegeneration

HLA Genetic Variation

HLA genetic variation has been found to confer risk for a wide variety of diseases. Identifying these associations and understanding their molecular mechanisms is ongoing and holds promise for the development of therapeutics. Find the latest research on HLA genetic variation here.

Super-resolution Microscopy

Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Here are the latest discoveries pertaining to super-resolution microscopy.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

Brain Lower Grade Glioma

Low grade gliomas in the brain form from oligodendrocytes and astrocytes and are the slowest-growing glioma in adults. Discover the latest research on these brain tumors here.

CD4/CD8 Signaling

Cluster of differentiation 4 and 8 (CD8 and CD8) are glycoproteins founds on the surface of immune cells. Here is the latest research on their role in cell signaling pathways.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Related Papers

Plant Physiology
Douglas E Soltis, Pamela S Soltis
Trends in Genetics : TIG
R ZardoyaA Meyer
Molecular Biology and Evolution
Jonathan P Bollback
© 2020 Meta ULC. All rights reserved