Circadian rhythms are generated by cell-autonomous transcriptional feedback loops composed of positive transcriptional activators and negative feedback elements, resulting in rhythmic expression of several core clock genes and numerous clock-controlled genes (CCGs). Besides the core circadian feedback elements, numerous transcriptional and post-transcriptional regulators have been shown to be involved in the oscillations of core clock genes and CCGs.
With the aim of fulfilling the growing need for data mining from the genome-wide circadian datasets available, we developed CirGRDB by integrating more than 4,936 genome-wide assays from 96 circadian profiling datasets. It presents a friendly web interface that allows users to search, browse and annotate circadian genes and their regulators, including as follows:
- Temporal expression patterns of circadian genes in 12 human tissues/cell lines (Dorsolateral prefrontal cortex, Anterior cingulate cortex, Hippocampus, Amygdala, Nucleus accumbens, Cerebellum, Islet, Epidermal stem cell, etc.) and 25 mouse tissues/cell lines based on 4,508 collected genome-wide circadian transcriptional profiling assays;
- Cycling genes related to 3 clinical disorders including sleep disorder, aging, tumor, and corresponding abnormal expression patterns;
- Eight kinds of transcriptional and post-transcriptional regulators involved in the rhythmic expression of the specific genes, including transcription factors, histone modifications, chromatin accessibility, enhancer RNAs, miRNAs, RNA-binding proteins, RNA editing and RNA methylation;
- Abnormal expression patterns of cycling genes under the loss function of 17 regulators;
- Network constructed based on regulatory factors and protein-protein interactions.
Li X, Shi L, Zhang K, Wei W, Liu Q, Mao F, Li J, Cai W, Chen H, Teng H, Li J and Sun ZS. CirGRDB: a database for the genome-wide deciphering circadian genes and regulators. Nucleic Acids Res. 2017. doi: https://doi.org/10.1093/nar/gkx944.
News and Updates
- 03 Oct. 2017
08:50CirGRDB was accepted by Nucleic Acids Research.
- 20 Sep. 2017
18:31Updates all re-calculated data sets.
- 2 Sep. 2017
10:15QC & Re-normalize Microarray data sets with RMA method.
- 21 June. 2017
09:20Collection 19 tissues/cell line of mouse or human data sets from ArrayExpress database.
- 01 Feb. 2017
10:15Visualiztion of rhythmic genes and their regulatory elements.
- 25 Dec. 2016
15:40Version 1.0 of the database is online.
- 04 Oct. 2016