Circadian clock exists endogenously in almost every organism and drives oscillatory changes in a myriad of behavioral and physiological processes. Depending on the organism and cell type, the circadian clock promotes rhythmic expression of 1% to over 60% of the genome, serving as the molecular basis for rhythmic control at the system’s level (Li et al., 2015). The CGDB (Circadian Gene DataBase) is an online resource containing over 72,800 genes in more than 148 organisms that exhibit (or may exhibit) daily oscillation at the transcript level. These include 1,382 genes with oscillatory transcripts that have been experimentally validated by techniques including RT-PCR, Northern blot, and in situ hybridization. Because the same gene often exhibits different pattern of temporal expression in different tissues/cells of an organism, and within an organism each tissue/cell type has a unique set of genes that show oscillation at the transcript level (Zhang et al., 2014), we have indicated the phase (time of peak and trough expression) of the oscillation for each gene and the tissue/cell type in which it was identified to be cycling. We have also calculated the amplitude of the oscillation by dividing the peak value with the trough value. Ortholog search for these genes identified another 44,836 which are included in the database as potentially oscillating genes. In addition, we have incorporated 26,582 cycling genes identified in transcriptome profiling studies using microarray or RNA-sequencing. Since post-translational modifications (PTMs) play a key role in regulating circadian timing (Diernfelner et al., 2011; Hardin et al., 2011; Kusakina et al., 2012; Lowrey et al., 2011), we have integrated known PTM sites from published databases including dbPAF (Ullah et al., 2016), dbPPT (Cheng et al., 2014), and CPLM (Liu et al., 2014). All in all, CGDB can serve as a tool to search for genes with oscillatory expression and identify new cycling genes.
For publication of results please cite the following articles:
CGDB: a database of circadian genes in eukaryotes
Shujing Li, Ke Shui, Ying Zhang, Yongqiang Lv, Wankun Deng, Shahid Ullah, Luoying Zhang and Yu Xue. Nucleic Acids Res. 2016; 10.1093/nar/gkw1028