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Nucleic Acids Research·· 4 小时前AI 评分55

CircaVal 发布面向基因的多组学昼夜节律调控平台

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

AI 导读

CircaVal 是一个以基因为中心的多组学平台,用于整合探索人类、小鼠和狒狒的昼夜节律调控特征。平台用标准化的、按数据类型区分的流程处理公共数据集,并把基因节律性与组织特异表达、跨物种直系同源、功能注释和多组学调控特征整合在一起。研究团队提出整合节律评分(IRS),把多种节律检测方法之间的一致性同独立数据集间的可重复性结合起来,为候选节律基因的优先级排序提供定量依据。用户可跨数据集查看基因节律性、识别组织富集的节律基因、比较物种间节律性并探索相关调控特征,还能对自行上传的时间序列数据做节律分析,并通过程序化接口访问数据。平台在 CircaVal.com 免费开放。

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来源:Nucleic Acids Research · doi.org

论文摘要

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.