Repeatability of published microarray gene expression analyses

Four teams of analysts attempted exact reproduction of results of 18 microarray experiments published in the journal in 2005–2006 using the data and analytical methods detailed in the original publications. In addition to MIAME criteria, the authors recommend publication of an explicit record of the...

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Vydané v:	Nature genetics Ročník 41; číslo 2; s. 149 - 155
Hlavní autori:	Ioannidis, John P A, Allison, David B, Ball, Catherine A, Coulibaly, Issa, Cui, Xiangqin, Culhane, Aedín C, Falchi, Mario, Furlanello, Cesare, Game, Laurence, Jurman, Giuseppe, Mangion, Jon, Mehta, Tapan, Nitzberg, Michael, Page, Grier P, Petretto, Enrico, van Noort, Vera
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	New York Nature Publishing Group US 01.02.2009 Nature Publishing Group
Predmet:	Agriculture Analysis Animal Genetics and Genomics Animals Arrays Biological and medical sciences Biomedical and Life Sciences Biomedical research Biomedicine Cancer Research Data Interpretation, Statistical Data processing Databases, Genetic DNA microarrays Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling - standards Gene Function Genetic research Genetics Genetics of eukaryotes. Biological and molecular evolution Genome-Wide Association Study - standards Human Genetics Humans Methods Oligonucleotide Array Sequence Analysis - standards Peer Review, Research Publications - standards Reproducibility of Results United States United Kingdom Gene expression Microarray
ISSN:	1061-4036, 1546-1718, 1546-1718
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Abstract	Four teams of analysts attempted exact reproduction of results of 18 microarray experiments published in the journal in 2005–2006 using the data and analytical methods detailed in the original publications. In addition to MIAME criteria, the authors recommend publication of an explicit record of the analytical protocols used. Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005–2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.
AbstractList	Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered. [PUBLICATION ABSTRACT] Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered. Four teams of analysts attempted exact reproduction of results of 18 microarray experiments published in the journal in 2005–2006 using the data and analytical methods detailed in the original publications. In addition to MIAME criteria, the authors recommend publication of an explicit record of the analytical protocols used. Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005–2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered. Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.
Audience	Academic
Author	Game, Laurence Ioannidis, John P A Furlanello, Cesare Cui, Xiangqin Jurman, Giuseppe Allison, David B Coulibaly, Issa Mehta, Tapan Culhane, Aedín C Nitzberg, Michael Mangion, Jon Page, Grier P Falchi, Mario Petretto, Enrico Ball, Catherine A van Noort, Vera
Author_xml	– sequence: 1 givenname: John P A surname: Ioannidis fullname: Ioannidis, John P A email: jioannid@cc.uoi.gr organization: Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, University of Ioannina School of Medicine, Biomedical Research Institute, Foundation for Research and Technology–Hellas, Tufts Medical Center and Department of Medicine, Center for Genetic Epidemiology and Modeling, Tufts University School of Medicine – sequence: 2 givenname: David B surname: Allison fullname: Allison, David B organization: Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham – sequence: 3 givenname: Catherine A surname: Ball fullname: Ball, Catherine A organization: Department of Biochemistry, Stanford University School of Medicine – sequence: 4 givenname: Issa surname: Coulibaly fullname: Coulibaly, Issa organization: Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham – sequence: 5 givenname: Xiangqin surname: Cui fullname: Cui, Xiangqin organization: Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham – sequence: 6 givenname: Aedín C surname: Culhane fullname: Culhane, Aedín C organization: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Department of Biostatistics, Harvard School of Public Health – sequence: 7 givenname: Mario surname: Falchi fullname: Falchi, Mario organization: Genomic Medicine, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Department of Twin Research & Genetic Epidemiology, St. Thomas' Campus, King's College London – sequence: 8 givenname: Cesare surname: Furlanello fullname: Furlanello, Cesare organization: Fondazione Bruno Kessler, via Sommarive 18 – sequence: 9 givenname: Laurence surname: Game fullname: Game, Laurence organization: Medical Research Council Clinical Sciences Centre Microarray Centre, Hammersmith Hospital – sequence: 10 givenname: Giuseppe surname: Jurman fullname: Jurman, Giuseppe organization: Fondazione Bruno Kessler, via Sommarive 18 – sequence: 11 givenname: Jon surname: Mangion fullname: Mangion, Jon organization: Medical Research Council Clinical Sciences Centre Microarray Centre, Hammersmith Hospital – sequence: 12 givenname: Tapan surname: Mehta fullname: Mehta, Tapan organization: Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham – sequence: 13 givenname: Michael surname: Nitzberg fullname: Nitzberg, Michael organization: Department of Biochemistry, Stanford University School of Medicine – sequence: 14 givenname: Grier P surname: Page fullname: Page, Grier P organization: Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Statistics and Epidemiology Unit, RTI International – sequence: 15 givenname: Enrico surname: Petretto fullname: Petretto, Enrico organization: Medical Research Council Clinical Sciences Centre Microarray Centre, Hammersmith Hospital, Department of Epidemiology, Public Health and Primary Care, Faculty of Medicine, Imperial College – sequence: 16 givenname: Vera surname: van Noort fullname: van Noort, Vera organization: European Molecular Biology Laboratory Heidelberg
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Snippet	Four teams of analysts attempted exact reproduction of results of 18 microarray experiments published in the journal in 2005–2006 using the data and analytical... Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals...
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SubjectTerms	Agriculture Analysis Animal Genetics and Genomics Animals Arrays Biological and medical sciences Biomedical and Life Sciences Biomedical research Biomedicine Cancer Research Data Interpretation, Statistical Data processing Databases, Genetic DNA microarrays Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling - standards Gene Function Genetic research Genetics Genetics of eukaryotes. Biological and molecular evolution Genome-Wide Association Study - standards Human Genetics Humans Methods Oligonucleotide Array Sequence Analysis - standards Peer Review, Research Publications - standards Reproducibility of Results
Title	Repeatability of published microarray gene expression analyses
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