Cis-Cardio: A comprehensive analysis platform for cardiovascular-relavant cis- regulation in human and mouse

Chao Song; Yuexin Zhang; Hong Huang; Yuezhu Wang; Xilong Zhao; Guorui Zhang; Mingxue Yin; Chenchen Feng; Qiuyu Wang; Fengcui Qian; Desi Shang; Jian Zhang; Jiaqi Liu; Chunquan Li; Huifang Tang

doi:10.1016/j.omtn.2023.07.030

Cis-Cardio: A comprehensive analysis platform for cardiovascular-relavant cis- regulation in human and mouse

Mol Ther Nucleic Acids. 2023 Jul 27:33:655-667. doi: 10.1016/j.omtn.2023.07.030. eCollection 2023 Sep 12.

Authors

Chao Song^{1

2

3

4

5}, Yuexin Zhang^{1

2

3

4

5}, Hong Huang^{1

2

3

5

6}, Yuezhu Wang⁷, Xilong Zhao⁷, Guorui Zhang^{1

2

3}, Mingxue Yin^{1

2

3}, Chenchen Feng⁷, Qiuyu Wang^{1

2

3

4

5

8

9}, Fengcui Qian^{1

2

3

4

5}, Desi Shang^{1

2

3

4

5

8

9}, Jian Zhang⁷, Jiaqi Liu^{1

2

3

4

5}, Chunquan Li^{1

2

3

4

5

8

9

10

11}, Huifang Tang^{1

2

3

4

5

6}

Affiliations

¹ The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
² The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
³ Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, China.
⁴ School of Computer, University of South China, Hengyang, Hunan 421001, China.
⁵ The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, China.
⁶ Clinical Research Center for Myocardial Injury in Hunan Province, Hengyang, Hunan 421001, China.
⁷ School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
⁸ Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
⁹ Department of Cell Biology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
¹⁰ National Health Commission Key Laboratory of Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China.
¹¹ Key Laboratory of Rare Pediatric Diseases, Ministry of Education, University of South China, Hengyang, Hunan 421001, China.

Abstract

Cis-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 cis-regulatory data are urgent to decipher the potential mechanisms of cardiovascular diseases from a cis-regulatory element aspect. Here, we developed a novel web server, Cis-Cardio, which aims to document a large number of available cardiovascular-related cis-regulatory data and to provide analysis for unveiling the comprehensive mechanisms at a cis-regulation level. The current version of Cis-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, Cis-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, Cis-Cardio provides detailed and abundant (epi-) genetic annotations in cis-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, Cis-Cardio is a valuable resource for elucidating and analyzing regulatory cues of cardiovascular-specific cis-regulatory elements. The platform is freely available at http://www.licpathway.net/Cis-Cardio/index.html.

Keywords: MT: Bioinformatics; cardiovascular; cis-regulation; platform; transcription regulation.