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To unravel the complexity of the clinical phenotype\u2013genotype network, we used cardiovascular diseases (CVDs) and associated non-coding RNAs (ncRNAs) (i.e. miRNAs, long ncRNAs, etc.) as the case for the study of CVDs at a systems or network level. We first integrated a database of CVDs and ncRNAs (CVDncR, http:\/\/sysbio.org.cn\/cvdncr\/) to construct CVD\u2013ncRNA networks and annotate their clinical associations. To characterize the networks, we then separated the miRNAs into two groups, i.e. universal miRNAs associated with at least two types of CVDs and specific miRNAs related only to one type of CVD. Our analyses indicated two interesting patterns in these CVD\u2013ncRNA networks. First, scale-free features were present within both CVD\u2013miRNA and CVD\u2013lncRNA networks; second, universal miRNAs were more likely to be CVDs biomarkers. These results were confirmed by computational functional analyses. The findings offer theoretical guidance for decoding CVD\u2013ncRNA associations and will facilitate the screening of CVD ncRNA biomarkers.<\/jats:p><jats:p>Database URL: http:\/\/sysbio.org.cn\/cvdncr\/<\/jats:p>","DOI":"10.1093\/database\/baz147","type":"journal-article","created":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T12:11:20Z","timestamp":1576066280000},"source":"Crossref","is-referenced-by-count":10,"title":["Phenotype\u2013genotype network construction and characterization: a case study of cardiovascular diseases and associated non-coding RNAs"],"prefix":"10.1093","volume":"2020","author":[{"given":"Rongrong","family":"Wu","sequence":"first","affiliation":[{"name":"Center for Systems Biology, Soochow University, No. 199 Renai Road, Suzhou, Jiangsu 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuxin","family":"Lin","sequence":"additional","affiliation":[{"name":"Center for Systems Biology, Soochow University, No. 199 Renai Road, Suzhou, Jiangsu 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingyun","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Systems Biology, Soochow University, No. 199 Renai Road, Suzhou, Jiangsu 215123, China"},{"name":"Institutes for Systems Genetics, West China Hospital, Sichuan University, No. 17 Gaopeng Avenue, Ji Tai\u2019an Center, Chengdu, Sichuan 610041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chaoying","family":"Zhan","sequence":"additional","affiliation":[{"name":"Center for Systems Biology, Soochow University, No. 199 Renai Road, Suzhou, Jiangsu 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongxin","family":"He","sequence":"additional","affiliation":[{"name":"Center for Systems Biology, Soochow University, No. 199 Renai Road, Suzhou, Jiangsu 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manhong","family":"Shi","sequence":"additional","affiliation":[{"name":"Center for Systems Biology, Soochow University, No. 199 Renai Road, Suzhou, Jiangsu 215123, China"},{"name":"College of Information and Network Engineering, Anhui Science and Technology University, No. 9 Donghua Road, Fengyang, Anhui 233100, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhi","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, School of Medicine, Soochow University, No. 199 Renai Road, Suzhou, Jiangsu 215123, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bairong","family":"Shen","sequence":"additional","affiliation":[{"name":"Institutes for Systems Genetics, West China Hospital, Sichuan University, No. 17 Gaopeng Avenue, Ji Tai\u2019an Center, Chengdu, Sichuan 610041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,1,15]]},"reference":[{"key":"2020011607073979100_ref1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004747","article-title":"Understanding genotype-phenotype effects in cancer via network approaches","volume":"12","author":"Kim","year":"2016","journal-title":"PLoS Comput. 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