Skip to content
DraconiticResearch
Search Sources API
203,203 studies31 sourcesUpdated 46 min ago
Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

CircaVal: a gene-centric multi-omics platform for exploring circadian regulatory features

  • Guohao Han1,2
  • Xiaodie Wu1,2
  • Qian Li1,2
  • Runhe Shi1,2
  • Xiaoyun Xiao1,2
  • Jijun Liu1,2
  • Haisen Zhang1,2
  • Dengke Gao1,2
  • Chao Li1,2
  • Aihua Wang2,3
  • Yaping Jin1,2
  • Trees-Juen Chuang4
2 more authors
  • Hsu-Wen Chao5,6,7
  • Huatao Chen1,2
7 affiliations
  1. 1Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100 ,
  2. 2Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, Northwest A&F University , Yangling, Shaanxi 712100 ,
  3. 3Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100 ,
  4. 4Genomics Research Center , Academia Sinica, Taipei 115201 ,
  5. 5Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University , Taoyuan city 333323 ,
  6. 6Division of Hepato-Gastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine , Kaohsiung 833401 ,
  7. 7Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University , Kaohsiung 807378 ,
Open at sourcePDFDOICite

Abstract

The circadian clock orchestrates daily physiological processes through coordinated regulation of clock-controlled gene expression across multiple molecular layers. However, systematic characterization of this multilayered rhythmic regulation remains challenging because relevant information is distributed across independent datasets and rhythmicity is evaluated using diverse analytical approaches. Here, we developed CircaVal, a gene-centric multi-omics platform for the integrated exploration and interpretation of circadian regulatory features in humans, mice, and baboons. To support this framework, CircaVal processes public datasets using standardized, data-type-specific pipelines, and gene rhythmicity is integrated with tissue-specific expression, cross-species orthology, functional annotations, and multi-omics regulatory features. CircaVal further introduces an integrated rhythmicity score (IRS), which combines concordance across multiple rhythm-detection methods with reproducibility across independent datasets to provide a quantitative basis for prioritizing candidate rhythmic genes. The platform enables users to examine gene rhythmicity across datasets, identify tissue-enriched rhythmic genes, compare rhythmicity across species, and explore associated regulatory features. Additional functions include interactive gene-centric exploration, genome-browser visualization, rhythmicity analysis of user-uploaded time-series data, and programmatic data access. Together, these capabilities provide an integrated framework for rhythmic gene prioritization and gene-level interpretation of circadian regulatory features across tissues, species, datasets, and omics data types. CircaVal is freely available at https://CircaVal.com.

Related

  1. Exploring the transcriptional and post-transcriptional regulatory networks of methionine sulfoxide reductase B1 in breast cancer.
    Jingsong Cheng, Diyuan Zhang, Xue Chen +7
    Genes & diseasesPeer-reviewedCC BYFull textMolecular biology & gene regulationEurope PMC
  2. RNAactDrug 2.0: an updated resource for systematically exploring molecular features associated with drug sensitivity across multi-omics datasets
    Feng Li, Liying Pei, Jiangtao Xing +8
    Nucleic Acids ResearchPeer-reviewedCC BY 4.0Full textMolecular biology & gene regulationCrossref
  3. Exploring biomarkers and regulatory mechanisms associated with 20 protein post-translational modifications in acute myocardial infarction based on transcriptomics
    Jie Zhang, Binhe Li, Mengyue Yang +3
    Frontiers in Cardiovascular MedicinePeer-reviewedCC BY 4.0Full textMolecular biology & gene regulationCrossrefPMC
  4. Mapping Retinal Gene Expression to Cell Classes: Insights into Retinal Circadian Rhythms.
    Julia Buckland, Michael J Gilhooley, Mark W Hankins +2
    Clocks & sleepPeer-reviewedCC BYFull textMolecular biology & gene regulationEurope PMC
  5. Dietary selenium deficiency drives sex-specific circadian disturbance through redox imbalance and causes early systolic dysfunction in mice
    X. Guo, F. Lambregtse, L. Geerlings +8
    bioRxivPreprintCC BYFull textMolecular biology & gene regulationbioRxiv

Cite

BibTeXRIS
BibTeX
@article{han2026circaval,
  title = {{CircaVal: a gene-centric multi-omics platform for exploring circadian regulatory features}},
  author = {Guohao Han and Xiaodie Wu and Qian Li and Runhe Shi and Xiaoyun Xiao and Jijun Liu and Haisen Zhang and Dengke Gao and Chao Li and Aihua Wang and Yaping Jin and Trees-Juen Chuang and Hsu-Wen Chao and Huatao Chen},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = nov,
  doi = {10.1093/nar/gkag1090},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1090/9006194},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - CircaVal: a gene-centric multi-omics platform for exploring circadian regulatory features
AU  - Guohao Han
AU  - Xiaodie Wu
AU  - Qian Li
AU  - Runhe Shi
AU  - Xiaoyun Xiao
AU  - Jijun Liu
AU  - Haisen Zhang
AU  - Dengke Gao
AU  - Chao Li
AU  - Aihua Wang
AU  - Yaping Jin
AU  - Trees-Juen Chuang
AU  - Hsu-Wen Chao
AU  - Huatao Chen
PY  - 2026
DA  - 2026/11/02
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1090
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1090/9006194
AB  - The circadian clock orchestrates daily physiological processes through coordinated regulation of clock-controlled gene expression across multiple molecular layers. However, systematic characterization of this multilayered rhythmic regulation remains challenging because relevant information is distributed across independent datasets and rhythmicity is evaluated using diverse analytical approaches. Here, we developed CircaVal, a gene-centric multi-omics platform for the integrated exploration and interpretation of circadian regulatory features in humans, mice, and baboons. To support this framework, CircaVal processes public datasets using standardized, data-type-specific pipelines, and gene rhythmicity is integrated with tissue-specific expression, cross-species orthology, functional annotations, and multi-omics regulatory features. CircaVal further introduces an integrated rhythmicity score (IRS), which combines concordance across multiple rhythm-detection methods with reproducibility across independent datasets to provide a quantitative basis for prioritizing candidate rhythmic genes. The platform enables users to examine gene rhythmicity across datasets, identify tissue-enriched rhythmic genes, compare rhythmicity across species, and explore associated regulatory features. Additional functions include interactive gene-centric exploration, genome-browser visualization, rhythmicity analysis of user-uploaded time-series data, and programmatic data access. Together, these capabilities provide an integrated framework for rhythmic gene prioritization and gene-level interpretation of circadian regulatory features across tissues, species, datasets, and omics data types. CircaVal is freely available at https://CircaVal.com.
SN  - 0305-1048
SN  - 1362-4962
ER  -