Review Article: Stable feature selection for biomarker discovery
Computational Biology and Chemistry
Computational Biology and Chemistry
Stable Gene Selection from Microarray Data via Sample Weighting
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A Survey on Filter Techniques for Feature Selection in Gene Expression Microarray Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Warehousing re-annotated cancer genes for biomarker meta-analysis
Computer Methods and Programs in Biomedicine
Incorporation of gene exchangeabilities improves the reproducibility of gene set rankings
Computational Statistics & Data Analysis
Computers in Biology and Medicine
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Motivation: According 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. Results: We 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. Contact: guoz@ems.hrbmu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.