Song Chao, Zhang Yuexin, Huang Hong, Wang Yuezhu, Zhao Xilong, Zhang Guorui, Yin Mingxue, Feng Chenchen, Wang Qiuyu, Qian Fengcui, Shang Desi, Zhang Jian, Liu Jiaqi, Li Chunquan, Tang Huifang
The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Mol Ther Nucleic Acids. 2023 Jul 27;33:655-667. doi: 10.1016/j.omtn.2023.07.030. eCollection 2023 Sep 12.
-regulatory elements are important molecular switches in controlling gene expression and are regarded as determinant hubs in the transcriptional regulatory network. Collection and processing of large-scale -regulatory data are urgent to decipher the potential mechanisms of cardiovascular diseases from a -regulatory element aspect. Here, we developed a novel web server, -Cardio, which aims to document a large number of available cardiovascular-related -regulatory data and to provide analysis for unveiling the comprehensive mechanisms at a -regulation level. The current version of -Cardio catalogs a total of 45,382,361 genomic regions from 1,013 human and mouse epigenetic datasets, including ATAC-seq, DNase-seq, Histone ChIP-seq, TF/TcoF ChIP-seq, RNA polymerase ChIP-seq, and Cohesin ChIP-seq. Importantly, -Cardio provides six analysis tools, including region overlap analysis, element upstream/downstream analysis, transcription regulator enrichment analysis, variant interpretation, and protein-protein interaction-based co-regulatory analysis. Additionally, -Cardio provides detailed and abundant (epi-) genetic annotations in -regulatory regions, such as super-enhancers, enhancers, transcription factor binding sites (TFBSs), methylation sites, common SNPs, risk SNPs, expression quantitative trait loci (eQTLs), motifs, DNase I hypersensitive sites (DHSs), and 3D chromatin interactions. In summary, -Cardio is a valuable resource for elucidating and analyzing regulatory cues of cardiovascular-specific -regulatory elements. The platform is freely available at http://www.licpathway.net/Cis-Cardio/index.html.
调控元件是控制基因表达的重要分子开关，被视为转录调控网络中的决定性枢纽。从调控元件层面解析心血管疾病的潜在机制，迫切需要收集和处理大规模的调控数据。在此，我们开发了一种新型网络服务器——心血管调控元件分析工具（-Cardio），旨在整理大量可用的心血管相关调控数据，并提供分析以揭示调控层面的综合机制。-Cardio的当前版本编目了来自1013个人类和小鼠表观遗传数据集的总共45382361个基因组区域，包括ATAC-seq、DNase-seq、组蛋白ChIP-seq、转录因子/转录共因子ChIP-seq、RNA聚合酶ChIP-seq和黏连蛋白ChIP-seq。重要的是，-Cardio提供六种分析工具，包括区域重叠分析、元件上下游分析、转录调节因子富集分析、变异解读以及基于蛋白质-蛋白质相互作用的共调控分析。此外，-Cardio在调控区域提供详细且丰富的（表观）遗传注释，如超级增强子、增强子、转录因子结合位点（TFBSs）、甲基化位点、常见单核苷酸多态性（SNPs）、风险SNPs、表达数量性状位点（eQTLs）、基序、DNA酶I超敏位点（DHSs）和三维染色质相互作用。总之，-Cardio是阐明和分析心血管特异性调控元件调控线索的宝贵资源。该平台可在http://www.licpathway.net/Cis-Cardio/index.html免费获取。
