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Nucleic Acids Res. 2018 Jan 4;46(D1):D64-D70. doi: 10.1093/nar/gkx944.

CirGRDB: a database for the genome-wide deciphering circadian genes and regulators.

Author information

1
State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China.
2
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
3
Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
4
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
5
Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

Abstract

Circadian rhythms govern various kinds of physiological and behavioral functions of the living organisms, and disruptions of the rhythms are highly detrimental to health. Although several databases have been built for circadian genes, a resource for comprehensive post-transcriptional regulatory information of circadian RNAs and expression patterns of disease-related circadian RNAs is still lacking. Here, we developed CirGRDB (http://cirgrdb.biols.ac.cn) by integrating more than 4936 genome-wide assays, with the aim of fulfilling the growing need to understand the rhythms of life. CirGRDB presents a friendly web interface that allows users to search and browse temporal expression patterns of interested genes in 37 human/mouse tissues or cell lines, and three clinical disorders including sleep disorder, aging and tumor. More importantly, eight kinds of potential 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, can also be retrieved. Furthermore, a regulatory network could be generated based on the regulatory information. In summary, CirGRDB offers a useful repository for exploring disease-related circadian RNAs, and deciphering the transcriptional and post-transcriptional regulation of circadian rhythms.

PMID:
29059379
PMCID:
PMC5753205
DOI:
10.1093/nar/gkx944
[Indexed for MEDLINE]
Free PMC Article

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