ArticleBioinformatics (Oxford, England)2009
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed.
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- Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein.PLoS computational biology · 2020Article
- A qualitative transcriptional signature for the histological reclassification of lung squamous cell carcinomas and adenocarcinomas.BMC genomics · 2019Article
- A rank-based algorithm of differential expression analysis for small cell line data with statistical control.Briefings in bioinformatics · 2019Article
- Stability of methods for differential expression analysis of RNA-seq data.BMC genomics · 2019Article
- Identification of differentially expressed genes by means of outlier detection.BMC bioinformatics · 2018Article
- SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data.BMC systems biology · 2018Article
- Identifying differentially expressed genes from cross-site integrated data based on relative expression orderings.International journal of biological sciences · 2018Article
- Maximum Rank Reproducibility: A Nonparametric Approach to Assessing Reproducibility in Replicate Experiments.Journal of the American Statistical Association · 2018Article
- Discriminating cancer-related and cancer-unrelated chemoradiation-response genes for locally advanced rectal cancers.Scientific reports · 2016Article
- Development and validation of a custom microarray for global transcriptome profiling of the fungus Aspergillus nidulans.Current genetics · 2016Article
- Article
- A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies.Oncotarget · 2015Article
- Identification of reproducible drug-resistance-related dysregulated genes in small-scale cancer cell line experiments.Scientific reports · 2015Article
- Profile of differentially expressed intratumoral cytokines to predict the immune-polarizing side effects of tamoxifen in breast cancer treatment.American journal of cancer research · 2015Article
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10 authors.
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Abstract
motivationAccording to current consistency metrics such as percentage of overlapping genes (POG), lists of differentially expressed genes (DEGs) detected from different microarray studies for a complex disease are often highly inconsistent. This irreproducibility problem also exists in other high-throughput post-genomic areas such as proteomics and metabolism. A complex disease is often characterized with many coordinated molecular changes, which should be considered when evaluating the reproducibility of discovery lists from different studies.
resultsWe proposed metrics percentage of overlapping genes-related (POGR) and normalized POGR (nPOGR) to evaluate the consistency between two DEG lists for a complex disease, considering correlated molecular changes rather than only counting gene overlaps between the lists. Based on microarray datasets of three diseases, we showed that though the POG scores for DEG lists from different studies for each disease are extremely low, the POGR and nPOGR scores can be rather high, suggesting that the apparently inconsistent DEG lists may be highly reproducible in the sense that they are actually significantly correlated. Observing different discovery results for a disease by the POGR and nPOGR scores will obviously reduce the uncertainty of the microarray studies. The proposed metrics could also be applicable in many other high-throughput post-genomic areas.
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