Searching for Periodic Gene Expression Patterns Using Lomb-Scargle Periodograms

The Lomb-Scargle periodogram approach was applied to the search for periodically expressed genes in a Plasmodium falciparum dataset. The Lomb-Scargle algorithm has several computational advantages over more common approaches, such as Fourier analysis, including direct treatment of missing values and and a periodogram that has known statistical properties. Hierarchical clustering of periodograms shows explicit partitioning of multiple periodicities present in some gene expression patterns. The Lomb-Scargle algorithm performance was compared to earlier analysis of CAMDA 2004 challenge dataset by Bozdech et al. [1], based on Fast Fourier Transforms (FFT). We identified an additional 265 genes with 48-hr periodic expression, which were not considered by the FFT because they had too many missing values. We also automatically detected, in the same analysis, expression patterns with periodicity close to 24 hr, and other interesting patterns.