Dataset Information

A Complex Heterogeneous Network Model of Disease Regulated by Noncoding RNAs: A Case Study of Unstable Angina Pectoris.

ABSTRACT: MicroRNAs (miRNAs) are important types of noncoding RNAs, and there is a lack of holistic and systematic understanding of the functions they play in disease. We proposed a research strategy, including two parts network analysis and network modelling, to analyze, model, and predict the regulatory network of miRNAs from a network perspective, using unstable angina pectoris as an example. In the network analysis section, we proposed the WGCNA & SimCluster method using both correlation and similarity to find hub miRNAs, and validation on two datasets showed better results than the methods using correlation or similarity alone. In the network modelling section, we used six knowledge graph or graph neural network models for link prediction of three types of edges and multilabel classification of two types of nodes. Comparative experiments showed that the RotatE model was a good model for link prediction, while the RGCN model was the best model for multilabel classification. Potential target genes were predicted for hub miRNAs and validation of hub miRNA-target gene interactions, target genes as biomarkers and target gene functions were performed using a three-step validation approach. In conclusion, our study provides a new strategy to analyze and model miRNA regulatory networks.

SUBMITTER: Qi G

PROVIDER: S-EPMC9803582 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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A Complex Heterogeneous Network Model of Disease Regulated by Noncoding RNAs: A Case Study of Unstable Angina Pectoris.

Qi Guanpeng G Xu Ze Z Dan Hanyu H Jia Xiangnan X Jiang Qiang Q Zhang Aijun A Li Zhaohang Z Liu Xin X Ma Juman J Zheng Xiaosong X Li Zuojing Z

Computational intelligence and neuroscience 20221223

MicroRNAs (miRNAs) are important types of noncoding RNAs, and there is a lack of holistic and systematic understanding of the functions they play in disease. We proposed a research strategy, including two parts network analysis and network modelling, to analyze, model, and predict the regulatory network of miRNAs from a network perspective, using unstable angina pectoris as an example. In the network analysis section, we proposed the WGCNA & SimCluster method using both correlation and similarit ...[more]

PMID: 36590836

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Project description:Background: Salvia miltiorrhiza Bunge. [Lamiaceae, danshen] injection classes (SMIC) is widely used in the treatment of unstable angina (UA). However, it is uncertain which SMIC is more effective in terms of UA efficacy. The purpose of this Network Meta-analysis (NMA) was to compare the treatment effects of various SMIC to determine the best SMIC for the treatment of UA. Methods: The China National Knowledge Infrastructure (CNKI), Wanfang Database, China Science and Technology Journal Database (VIP), Chinese Biomedical Literature Database (CBM), PubMed, Web of Science, and Cochrane Library databases were searched to screen randomized controlled trials (RCTs) of SMIC for UA. The search time frame was all from the establishment of the database to May 2022. RevMan 5.3 and Stata 14.0 software were used for NMA. Results: A total of 148 studies including 14,979 patients, including 7,584 cases in the experimental group and 7,395 cases in the control group were included, and eight SMIC were extracted, namely:Danshen injection, Fufang Danshen injection, Guanxinning injection, Danshenchuanxiongqin injection, Danhong injection, Danshentong IIA Huangsuanna injection, Shenxiong Putaotang injection, and Danshenduofensuanyan injection. The results of NMA showed that, in terms of total effective rate, Shenxiong Putaotang injection and Danshenchuanxiongqin injection have the advantage; In terms of ECG efficiency, Danshentong IIA Huangsuanna injection and Danshen injection have an advantage; Danshenchuanxiongqin injection and Danshenduofensuanyan injection were more effective than other SMIC in improving angina pectoris attacks; Shenxiong Putaotang injection has an advantage in improving hs-CRP; Shenxiong Putaotang injection and Danshentong IIA Huangsuanna injection have advantages in improving TC and TG, respectively. Conclusion: The eight SMIC included in the current study were effective in treating UA, Shenxiong Putaotang injection and Danshentong IIA Huangsuanna injection were both superior in improving all outcome indicators. However, there is still a need for larger samples and high-quality randomized controlled trials for more refined comparisons of various SMIC. Systematic Review Registration: [PROSPERO], identifier [CRD42022350872].

Project description:Objective: Dazhu hongjingtian [DZHJT, Rhodiola wallichiana var. cholaensis (Praeger) S.H. Fu] preparation as an add-on therapy has been applied to the treatment of angina pectoris. We aimed to evaluate the efficacy and safety of DZHJT as adjuvant therapy for the treatment of unstable angina pectoris (UAP). Methods: An extensive literature search was conducted on PubMed, Emase, Cochrane Library, Wanfang, CNKI, and VIP databases from inception to January 2019. Randomized controlled trials (RCTs) comparing DZHJT in combination with Western medicine with Western medicine alone were included. Two authors independently performed the literature search, data extraction and risk of bias assessment of included studies, and conducted the statistical analysis. Results: A total of 18 RCTs involving 1,679 patients were included in the meta-analysis. Adjuvant treatment with DZHJT significantly decreased ≥80% reduction in the frequency of angina attacks [risk ratio (RR) 1.57; 95% CI 1.36-1.81], weekly frequency of angina attacks [mean difference (MD) -1.03 times; 95% confidence interval (CI) -1.51 to -0.55], marked improved abnormal electrocardiogram (RR 1.46; 95% CI 1.23-1.74). In addition, DZHJT significantly reduced the whole-blood viscosity (MD -0.70 mPa.s; 95% CI -0.84 to -0.55), plasma viscosity (MD -0.28 mPa.s; 95% CI -0.38 to -0.19), serum level of fibrinogen (MD -0.67 g/L; 95% CI -0.79 to -0.54), thromboxanes B2 (MD -14.01 ng/L; 95% CI -20.86 to -7.15), and C-reactive protein (MD -1.48 mg/L; 95% CI -2.72 to -0.25). No significant differences in headache/dizziness (RR 0.72; 95% CI 0.31-1.67) were observed between two groups. Conclusion: Adjuvant treatment with DZHJT has an add-on effect in reducing angina pectoris attacks in patients with UAP. The beneficial effect may be correlated with regulating whole-blood viscosity, plasma viscosity, fibrinogen, thromboxanes B2, and CRP level. However, future well-designed prospective, randomized, double-blind placebo-controlled trials with large sample sizes are required to evaluate the evidence.

Dataset Information

A Complex Heterogeneous Network Model of Disease Regulated by Noncoding RNAs: A Case Study of Unstable Angina Pectoris.

Publications

A Complex Heterogeneous Network Model of Disease Regulated by Noncoding RNAs: A Case Study of Unstable Angina Pectoris.

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