Repeatability of published microarray gene expression analyses

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.

A reputation economy: how individual reward considerations trump systemic arguments for open access to data

“…Insufficient data documentation has often been discussed as a major obstacle for replication studies (Ioannidis et al, 2009;Peters et al, 2016;Munafò et al, 2017). A way to increase the reproducibility of research could, therefore, be the implementation and adoption of data documentation and availability policies by scientific journals and funding agencies.…”

“…In a study from 2009, Ioannidis et al (2009) investigated 18 published and peerreviewed research articles on microarray studies. Even though all articles featured some form of data, the authors were only able to reproduce two studies.…”

Gene expression profiling in AML with normal karyotype can predict mutations for molecular markers and allows novel insights into perturbed biological pathways

“…18 This is an important result as many microarray gene expression signatures are difficult to reproduce given the complexity of microarray-based expression studies. 19 In contrast, FLT3-ITD does not provide a clear-cut AML subtype according to respective gene expression data. Our results further allowed novel biological insights into perturbed pathways associated with molecular markers in AML-NK.…”

Multilayer network modeling of integrated biological systems

“…Despite the success of multilayer network modeling and analysis in systems biology and systems medicine, some methodological challenges are still to be tackled to build consistent, replicable and reproducible [34,35,36,37] representations of multi-omics, connectomics and intercellular interactions as the ones central to the review of Gosak et al [1].…”