Identification of under-detected periodicity in time-series microarray data by using empirical mode decomposition.
Detecting periodicity signals from time-series microarray data is commonly used to facilitate the understanding of the critical roles and underlying mechanisms of regulatory transcriptomes. However, time-series microarray data are noisy. How the temporal data structure affects the performance of periodicity detection has remained elusive. We present a novel method based on empirical mode decomposition (EMD) to examine this effect. We applied EMD to a yeast microarray dataset and extracted a series of intrinsic mode function (IMF) oscillations from the time-series data. Our analysis indicated that many periodically expressed genes might have been under-detected in the original analysis because of interference between decomposed IMF oscillations. By validating a protein complex coexpression analysis, we revealed that 56 genes were newly determined as periodic. We demonstrated that EMD can be used incorporating with existing periodicity detection methods to improve their performance. This approach can be applied to other time-series microarray studies.
Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan.
Chaang-Ray
CR
Chen
Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan.
Wun-Yi
WY
Shu
Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan.
Cheng-Wei
CW
Chang
Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan.
Ian C
IC
Hsu
D066264:Datasets as Topic; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D010084:Oxidation-Reduction; D015203:Reproducibility of Results; D015003:Yeasts / Q000235:genetics / Q000378:metabolism