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Peters MJ, Joehanes R, Pilling LC, Schurmann C, Conneely KN, Powell J, Reinmaa E, Sutphin GL, Zhernakova A, Schramm K, Wilson YA, Kobes S, Tukiainen T, Ramos YF, Göring HHH, Fornage M, Liu Y, Gharib SA, Stranger BE, De Jager PL, Aviv A, Levy D, Murabito JM, Munson PJ, Huan T, Hofman A, Uitterlinden AG, Rivadeneira F, van Rooij J, Stolk L, Broer L, Verbiest MMPJ, Jhamai M, Arp P, Metspalu A, Tserel L, Milani L, Samani NJ, Peterson P, Kasela S, Codd V, Peters A, Ward-Caviness CK, Herder C, Waldenberger M, Roden M, Singmann P, Zeilinger S, Illig T, Homuth G, Grabe HJ, Völzke H, Steil L, Kocher T, Murray A, Melzer D, Yaghootkar H, Bandinelli S, Moses EK, Kent JW, Curran JE, Johnson MP, Williams-Blangero S, Westra HJ, McRae AF, Smith JA, Kardia SLR, Hovatta I, Perola M, Ripatti S, Salomaa V, Henders AK, Martin NG, Smith AK, Mehta D, Binder EB, Nylocks KM, Kennedy EM, Klengel T, Ding J, Suchy-Dicey AM, Enquobahrie DA, Brody J, Rotter JI, Chen YDI, Houwing-Duistermaat J, Kloppenburg M, Slagboom PE, Helmer Q, den Hollander W, Bean S, Raj T, Bakhshi N, Wang QP, Oyston LJ, Psaty BM, Tracy RP, Montgomery GW, Turner ST, Blangero J, Meulenbelt I, Ressler KJ, Yang J, Franke L, Kettunen J, Visscher PM, Neely GG, Korstanje R, Hanson RL, Prokisch H, Ferrucci L, Esko T, Teumer A, van Meurs JBJ, Johnson AD. The transcriptional landscape of age in human peripheral blood. Nat Commun 2015; 6:8570. [PMID: 26490707 PMCID: PMC4639797 DOI: 10.1038/ncomms9570] [Citation(s) in RCA: 407] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 09/07/2015] [Indexed: 02/08/2023] Open
Abstract
Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the ‘transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts. Ageing increases the risk of many diseases. Here the authors compare blood cell transcriptomes of over 14,000 individuals and identify a set of about 1,500 genes that are differently expressed with age, shedding light on transcriptional programs linked to the ageing process and age-associated diseases.
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Affiliation(s)
- Marjolein J Peters
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Roby Joehanes
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Luke C Pilling
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - Claudia Schurmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany.,The Charles Bronfman Institute for Personalized Medicine, Genetics of Obesity &Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York 10029, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia 30301, USA
| | - Joseph Powell
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Queensland 4000, Australia.,The Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4000, Australia
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - George L Sutphin
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands
| | - Katharina Schramm
- Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.,Institute of Human Genetics, Technical University Munich, Munich 85540, Germany
| | - Yana A Wilson
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sayuko Kobes
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona 85001, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | | | - Yolande F Ramos
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Myriam Fornage
- Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Sciences, Center at Houston, Texas 77001, USA.,Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, Texas 77001, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, Washington 98101, USA
| | - Barbara E Stranger
- Section of Genetic Medicine, Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois 60290, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Abraham Aviv
- Center of Human Development and Aging, New Jersey Medical School, Newark 07101, USA
| | - Daniel Levy
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Joanne M Murabito
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,General Internal Medicine Section, Boston University, Boston, Massachusetts 02108, USA
| | - Peter J Munson
- The Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20817, USA
| | - Tianxiao Huan
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Linda Broer
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Michael M P J Verbiest
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Mila Jhamai
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Pascal Arp
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Liina Tserel
- Molecular Pathology, Institute of Biomedicine, University of Tartu, Tartu 0794, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1, UK.,National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE1, UK
| | - Pärt Peterson
- Molecular Pathology, Institute of Biomedicine, University of Tartu, Tartu 0794, Estonia
| | - Silva Kasela
- Institute of Molecular and Cell Biology, Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1, UK.,National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE1, UK
| | - Annette Peters
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Cavin K Ward-Caviness
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Christian Herder
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf 40593, Germany
| | - Melanie Waldenberger
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Michael Roden
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf 40593, Germany.,Division of Endocrinology and Diabetology, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf 40593, Germany
| | - Paula Singmann
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Sonja Zeilinger
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover 30519, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Hans-Jörgen Grabe
- Department of Psychiatry and Psychotherapy, Helios Hospital Stralsund, University Medicine Greifswald, Greifswald 17489, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Leif Steil
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Thomas Kocher
- Unit of Periodontology, Department of Restorative Dentistry, Periodontology and Endodontology, University Medicine Greifswald, Greifswald 17489, Germany
| | - Anna Murray
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - David Melzer
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | | | - Eric K Moses
- Centre for Genetic Origins of Health and Disease, The University of Western Australia, and Faculty of Health Sciences, Curtin University, Perth, Western Australia 9011, Australia
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Joanne E Curran
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Matthew P Johnson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | | | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge 02138, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02108, USA
| | - Allan F McRae
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48103, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48103, USA
| | - Iiris Hovatta
- Department of Biosciences, University of Helsinki, Helsinki 00100, Finland.,Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki 00100, Finland
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB4, UK.,Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki 00100, Finland
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | - Anjali K Henders
- The Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4000, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4000, Australia
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Divya Mehta
- Max-Planck Institute of Psychiatry, Munich 80331, Germany
| | | | - K Maria Nylocks
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Elizabeth M Kennedy
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia 30301, USA
| | | | - Jingzhong Ding
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Astrid M Suchy-Dicey
- Department of Epidemiology, University of Washington, Seattle, Washington 98101, USA
| | - Daniel A Enquobahrie
- Department of Epidemiology, University of Washington, Seattle, Washington 98101, USA
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington 98101, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90501, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90501, USA
| | | | - Margreet Kloppenburg
- Department of Rheumatology, Leiden University Medical Center, Leiden 2300RC, The Netherlands.,Department of Clinical Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Quinta Helmer
- Department of Medical Statistics, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Wouter den Hollander
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Shannon Bean
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Towfique Raj
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02138, USA
| | - Noman Bakhshi
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Qiao Ping Wang
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lisa J Oyston
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA.,Cardiovascular Health Research Unit, Department of Health Services, University of Washington, Seattle, Washington 98195, USA.,Group Health Research Institute, Group Health Cooperative, Seattle, Washington 98195, USA
| | - Russell P Tracy
- Department of Pathology, University of Vermont College of Medicine, Colchester, Vermont 98195, USA
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4000, Australia
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55901, USA
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Ingrid Meulenbelt
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Jian Yang
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands
| | - Johannes Kettunen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland.,Computational Medicine, Institute of Health Sciences, Faculty of Medicine, University of Oulu, Oulu 90570, Finland
| | - Peter M Visscher
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - G Gregory Neely
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ron Korstanje
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona 85001, USA
| | - Holger Prokisch
- Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.,Institute of Human Genetics, Technical University Munich, Munich 85540, Germany
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland 21218, USA
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge 02138, USA.,Division of Endocrinology, Children's Hospital Boston, Boston, Massachusetts 02108, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Alexander Teumer
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Andrew D Johnson
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
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