Evidence map›Paper›PMID 19174838›Full record

ArticleNature genetics2009

Repeatability of published microarray gene expression analyses.

John P A Ioannidis, David B Allison, Catherine A Ball, Issa Coulibaly, Xiangqin Cui, Aedín C Culhane, Mario Falchi, Cesare Furlanello, Laurence Game, Giuseppe Jurman and 6 more

Abstract readEvaluation Study
PubMed Publisher
In one paragraph

Article in Nature genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 231 papers, 12 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
231citing papers in PubMed, 12 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

231 citing papers in PubMed, 12 syntheses or guidelines pooled it.

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171 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors.

John P A IoannidisClinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina 45110, Greece. jioannid@cc.uoi.gr
David B Allison
Catherine A Ball
Issa Coulibaly
Xiangqin Cui
Aedín C Culhane
Mario Falchi
Cesare Furlanello
Laurence Game
Giuseppe Jurman
Jon Mangion
Tapan Mehta
Michael Nitzberg
Grier P Page
Enrico Petretto
Vera van Noort

Funding

Screening for Breast Cancer Using Molecular SignaturesR01CA098522 · NCI · H. LEE MOFFITT CANCER CTR &RES INST · PI YEATMAN, TIMOTHY J · 2003 to 2007
$2.8M
Medical Research Council MC_U120097112NCI NIH HHS R01 CA098522
6 · The paper itself

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.

Indexed as

Databases, GeneticPeer Review, ResearchAnimalsData Interpretation, StatisticalGene Expression ProfilingGenome-Wide Association StudyHumansOligonucleotide Array Sequence AnalysisPublicationsReproducibility of Results

Identifiers

PMID19174838

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.