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...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Nature genetics Jg. 41; H. 2; S. 149 - 155
Hauptverfasser: 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
Format: Journal Article
Sprache:Englisch
Veröffentlicht: New York Nature Publishing Group US 01.02.2009
Nature Publishing Group
Schlagworte:
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
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung: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.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
content type line 14
ObjectType-Article-2
ObjectType-Undefined-1
ObjectType-Feature-3
content type line 23
ISSN:1061-4036
1546-1718
1546-1718
DOI:10.1038/ng.295