Detecting Periodic Genes from Irregularly Sampled Gene Expressions
Author Information
Author(s): Wentao Zhao, Kwadwo Agyepong, Erchin Serpedin, Edward R Dougherty
Primary Institution: Texas A&M University
Hypothesis
Do technically more sophisticated schemes, such as MAPES, achieve a better performance on real biological data sets than on simpler schemes?
Conclusion
The simplest method, Lomb-Scargle, outperforms more sophisticated Capon and MAPES methods in identifying periodically expressed genes.
Supporting Evidence
- Lomb-Scargle method identified the highest number of true positives.
- MAPES was the least effective in identifying cell cycle genes.
- The study utilized in silico experiments to validate the methods.
- 149 genes were identified as periodically expressed in Drosophila melanogaster.
Takeaway
This study compares different methods to find genes that turn on and off in cycles. The simplest method worked best.
Methodology
The study compares Lomb-Scargle, Capon, and MAPES methods using in silico experiments on gene expression data.
Limitations
The computational complexity of MAPES is not justifiable for small sample sizes, and the study is limited to specific datasets.
Participant Demographics
The study uses gene expression data from Saccharomyces cerevisiae and Drosophila melanogaster.
Digital Object Identifier (DOI)
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