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Luo L, Tan Z, Wang S. RSANMDA: Resampling based subview attention network for miRNA-disease association prediction. Methods 2024:S1046-2023(24)00169-5. [PMID: 39097178 DOI: 10.1016/j.ymeth.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/16/2024] [Accepted: 07/23/2024] [Indexed: 08/05/2024] Open
Abstract
Many studies have demonstrated the importance of accurately identifying miRNA-disease associations (MDAs) for understanding disease mechanisms. However, the number of known MDAs is significantly fewer than the unknown pairs. Here, we propose RSANMDA, a subview attention network for predicting MDAs. We first extract miRNA and disease features from multiple similarity matrices. Next, using resampling techniques, we generate different subviews from known MDAs. Each subview undergoes multi-head graph attention to capture its features, followed by semantic attention to integrate features across subviews. Finally, combining raw and training features, we use a multilayer scoring perceptron for prediction. In the experimental section, we conducted comparative experiments with other advanced models on both HMDD v2.0 and HMDD v3.2 datasets. We also performed a series of ablation studies and parameter tuning exercises. Comprehensive experiments conclusively demonstrate the superiority of our model. Case studies on lung, breast, and esophageal cancers further validate our method's predictive capability for identifying disease-related miRNAs.
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Affiliation(s)
- Longfei Luo
- Department of Computer Science and Engineering, School of Information Science and Engineering,Yunnan University, Kunming, 650504, Yunnan, China
| | - Zhuokun Tan
- Department of Computer Science and Engineering, School of Information Science and Engineering,Yunnan University, Kunming, 650504, Yunnan, China
| | - Shunfang Wang
- Department of Computer Science and Engineering, School of Information Science and Engineering,Yunnan University, Kunming, 650504, Yunnan, China.
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Wang W, Chen H. Predicting miRNA-disease associations based on lncRNA-miRNA interactions and graph convolution networks. Brief Bioinform 2023; 24:6918743. [PMID: 36526276 DOI: 10.1093/bib/bbac495] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 12/23/2022] Open
Abstract
Increasing studies have proved that microRNAs (miRNAs) are critical biomarkers in the development of human complex diseases. Identifying disease-related miRNAs is beneficial to disease prevention, diagnosis and remedy. Based on the assumption that similar miRNAs tend to associate with similar diseases, various computational methods have been developed to predict novel miRNA-disease associations (MDAs). However, selecting proper features for similarity calculation is a challenging task because of data deficiencies in biomedical science. In this study, we propose a deep learning-based computational method named MAGCN to predict potential MDAs without using any similarity measurements. Our method predicts novel MDAs based on known lncRNA-miRNA interactions via graph convolution networks with multichannel attention mechanism and convolutional neural network combiner. Extensive experiments show that the average area under the receiver operating characteristic values obtained by our method under 2-fold, 5-fold and 10-fold cross-validations are 0.8994, 0.9032 and 0.9044, respectively. When compared with five state-of-the-art methods, MAGCN shows improvement in terms of prediction accuracy. In addition, we conduct case studies on three diseases to discover their related miRNAs, and find that all the top 50 predictions for all the three diseases have been supported by established databases. The comprehensive results demonstrate that our method is a reliable tool in detecting new disease-related miRNAs.
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Huang Z, Zhu L, Zhang Q, Zhao D, Yao J. Circular RNA hsa-circ-0005238 enhances trophoblast migration, invasion and suppresses apoptosis via the miR-370-3p/CDC25B axis. Front Med (Lausanne) 2022; 9:943885. [PMID: 36314002 PMCID: PMC9606333 DOI: 10.3389/fmed.2022.943885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
Abstract
Background Fetal growth restriction (FGR) is attributed to various maternal, fetal, and placental factors. Trophoblasts participate in the establishment and maintenance of pregnancy from implantation and placentation to providing nutrition to fetus. Studies have reported that impaired trophoblast invasion and proliferation are among factors driving development of FGR. Circular RNAs (circRNAs) can regulate trophoblast function. We assessed the significance of circRNAs underlying FGR development. Materials and methods Next generation sequencing (NGS) was carried out to quantify levels of circRNAs in placenta tissues with and without FGR. In vitro experiments including transfection, (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2Htetrazolium) (MTS) assays, flow cytometry analyses, Transwell assays, wound healing assays, western blotting, qRT-PCR, dual-luciferase assays, immunofluorescence staining, and RIP assay were performed. Results There were 18 differentially expressed circRNAs between FGR placentas and uncomplicated pregnancies, while levels of hsa-circ-0005238 were markedly low in FGR placentas. Our in vitro experiments further revealed that hsa-circ-0005238 suppressed apoptosis and enhanced proliferation, migration, invasion of trophoblast cell lines. The hsa-miR-370-3p was identified as a direct target of hsa-circ-0005238. Mechanistically, hsa-miR-370-3p prevents invasion as well as migration of trophoblast cells by downregulating CDC25B. Conclusion The hsa-circ-0005238 modulates FGR pathogenesis by inhibiting trophoblast cell invasion and migration through sponging hsa-miR-370-3p. Hence, targeting this circRNA may be an attractive strategy for FGR treatment.
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Affiliation(s)
- Zhuomin Huang
- Shenzhen Maternity and Child Healthcare Hospital, The First School of Clinical Medicine, Southern Medical University, Shenzhen, Guangdong, China
| | - Litong Zhu
- Department of Gynecology, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Quanfu Zhang
- Shenzhen Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen, Guangdong, China
| | - Depeng Zhao
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, Guangdong, China,Depeng Zhao,
| | - Jilong Yao
- Shenzhen Maternity and Child Healthcare Hospital, The First School of Clinical Medicine, Southern Medical University, Shenzhen, Guangdong, China,*Correspondence: Jilong Yao,
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Wang W, Chen H. Predicting miRNA-disease associations based on graph attention networks and dual Laplacian regularized least squares. Brief Bioinform 2022; 23:6645486. [PMID: 35849099 DOI: 10.1093/bib/bbac292] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 01/05/2023] Open
Abstract
Increasing biomedical evidence has proved that the dysregulation of miRNAs is associated with human complex diseases. Identification of disease-related miRNAs is of great importance for disease prevention, diagnosis and remedy. To reduce the time and cost of biomedical experiments, there is a strong incentive to develop efficient computational methods to infer potential miRNA-disease associations. Although many computational approaches have been proposed to address this issue, the prediction accuracy needs to be further improved. In this study, we present a computational framework MKGAT to predict possible associations between miRNAs and diseases through graph attention networks (GATs) using dual Laplacian regularized least squares. We use GATs to learn embeddings of miRNAs and diseases on each layer from initial input features of known miRNA-disease associations, intra-miRNA similarities and intra-disease similarities. We then calculate kernel matrices of miRNAs and diseases based on Gaussian interaction profile (GIP) with the learned embeddings. We further fuse the kernel matrices of each layer and initial similarities with attention mechanism. Dual Laplacian regularized least squares are finally applied for new miRNA-disease association predictions with the fused miRNA and disease kernels. Compared with six state-of-the-art methods by 5-fold cross-validations, our method MKGAT receives the highest AUROC value of 0.9627 and AUPR value of 0.7372. We use MKGAT to predict related miRNAs for three cancers and discover that all the top 50 predicted results in the three diseases are confirmed by existing databases. The excellent performance indicates that MKGAT would be a useful computational tool for revealing disease-related miRNAs.
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Affiliation(s)
- Wengang Wang
- School of Software, East China Jiaotong University, Nanchang 330013, China
| | - Hailin Chen
- School of Software, East China Jiaotong University, Nanchang 330013, China
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Zhong J, Zhou W, Kang J, Fang Z, Xie M, Xiao Q, Peng W. DNRLCNN: A CNN Framework for Identifying MiRNA-Disease Associations Using Latent Feature Matrix Extraction with Positive Samples. Interdiscip Sci 2022; 14:607-622. [PMID: 35428965 DOI: 10.1007/s12539-022-00509-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Emerging evidence indicates that miRNAs have strong relationships with many human diseases. Investigating the associations will contribute to elucidating the activities of miRNAs and pathogenesis mechanisms, and providing new opportunities for disease diagnosis and drug discovery. Therefore, it is of significance to identify potential associations between miRNAs and diseases. The existing databases about the miRNA-disease associations (MDAs) only provide the known MDAs, which can be regarded as positive samples. However, the unknown MDAs are not sufficient to regard as reliable negative samples. To deal with this uncertainty, we proposed a convolutional neural network (CNN) framework, named DNRLCNN, based on a latent feature matrix extracted by only positive samples to predict MDAs. First, by only considering the positive samples into the calculation process, we captured the latent feature matrix for complex interactions between miRNAs and diseases in low-dimensional space. Then, we constructed a feature vector for each miRNA and disease pair based on the feature representation. Finally, we adopted a modified CNN for the feature vector to predict MDAs. As a result, our model achieves better performance than other state-of-the-art methods which based CNN in fivefold cross-validation on both miRNA-disease association prediction task (average AUC of 0.9030) and miRNA-phenotype association prediction task (average AUC of 0. 9442). In addition, we carried out case studies on two human diseases, and all the top-50 predicted miRNAs for lung neoplasms are confirmed by HMDD v3.2 and dbDEMC 2.0 databases, 98% of the top-50 predicted miRNAs for heart failure are confirmed. The experiment results show that our model has the capability of inferring potential disease-related miRNAs.
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Affiliation(s)
- Jiancheng Zhong
- College of Information Science and Engineering, Hunan Normal University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Wubin Zhou
- College of Information Science and Engineering, Hunan Normal University, Changsha, 410083, China
| | - Jiedong Kang
- College of Information Science and Engineering, Hunan Normal University, Changsha, 410083, China
| | - Zhuo Fang
- College of Information Science and Engineering, Hunan Normal University, Changsha, 410083, China
| | - Minzhu Xie
- College of Information Science and Engineering, Hunan Normal University, Changsha, 410083, China
| | - Qiu Xiao
- College of Information Science and Engineering, Hunan Normal University, Changsha, 410083, China.
| | - Wei Peng
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, China.
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Chakraborty S, Nath D. A Study on microRNAs Targeting the Genes Overexpressed in Lung Cancer and their Codon Usage Patterns. Mol Biotechnol 2022; 64:1095-1119. [DOI: 10.1007/s12033-022-00491-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
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Dai Q, Chu Y, Li Z, Zhao Y, Mao X, Wang Y, Xiong Y, Wei DQ. MDA-CF: Predicting MiRNA-Disease associations based on a cascade forest model by fusing multi-source information. Comput Biol Med 2021; 136:104706. [PMID: 34371319 DOI: 10.1016/j.compbiomed.2021.104706] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 01/17/2023]
Abstract
MicroRNAs (miRNAs) are significant regulators in various biological processes. They may become promising biomarkers or therapeutic targets, which provide a new perspective in diagnosis and treatment of multiple diseases. Since the experimental methods are always costly and resource-consuming, prediction of disease-related miRNAs using computational methods is in great need. In this study, we developed MDA-CF to identify underlying miRNA-disease associations based on a cascade forest model. In this method, multi-source information was integrated to represent miRNAs and diseases comprehensively, and the autoencoder was utilized for dimension reduction to obtain the optimal feature space. The cascade forest model was then employed for miRNA-disease association prediction. As a result, the average AUC of MDA-CF was 0.9464 on HMDD v3.2 in five-fold cross-validation. Compared with previous computational methods, MDA-CF performed better on HMDD v2.0 with an average AUC of 0.9258. Moreover, MDA-CF was implemented to investigate colon neoplasm, breast neoplasm, and gastric neoplasm, and 100%, 86%, 88% of the top 50 potential miRNAs were validated by authoritative databases. In conclusion, MDA-CF appears to be a reliable method to uncover disease-associated miRNAs. The source code of MDA-CF is available at https://github.com/a1622108/MDA-CF.
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Affiliation(s)
- Qiuying Dai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanyi Chu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhiqi Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yusong Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueying Mao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanjing Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, China.
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Nazarov PV, Kreis S. Integrative approaches for analysis of mRNA and microRNA high-throughput data. Comput Struct Biotechnol J 2021; 19:1154-1162. [PMID: 33680358 PMCID: PMC7895676 DOI: 10.1016/j.csbj.2021.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Review on tools and databases linking miRNA and its mRNA targetome. Databases show little overlap in miRNA targetome predictions suggesting strong contextual effects. Deconvolution and deep learning approaches are promising new approaches to improve miRNA targetome predictions.
Advanced sequencing technologies such as RNASeq provide the means for production of massive amounts of data, including transcriptome-wide expression levels of coding RNAs (mRNAs) and non-coding RNAs such as miRNAs, lncRNAs, piRNAs and many other RNA species. In silico analysis of datasets, representing only one RNA species is well established and a variety of tools and pipelines are available. However, attaining a more systematic view of how different players come together to regulate the expression of a gene or a group of genes requires a more intricate approach to data analysis. To fully understand complex transcriptional networks, datasets representing different RNA species need to be integrated. In this review, we will focus on miRNAs as key post-transcriptional regulators summarizing current computational approaches for miRNA:target gene prediction as well as new data-driven methods to tackle the problem of comprehensively and accurately dissecting miRNome-targetome interactions.
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Key Words
- CCA, canonical correlation analysis
- CDS, coding sequence
- CLASH, cross-linking, ligation and sequencing of hybrids
- CLIP, cross-linking immunoprecipitation
- CNN, convolutional neural network
- Data integration
- GO, gene ontology
- ICA, independent component analysis
- Matrix factorization
- NGS, next-generation sequencing
- NMF, non-negative matrix factorization
- PCA, principal component analysis
- RNASeq, high-throughput RNA sequencing
- TDMD, target RNA-directed miRNA degradation
- TF, transcription factors
- Target prediction
- Transcriptomics
- circRNA, circular RNA
- lncRNA, long non-coding RNA
- mRNA, messenger RNA
- miRNA, microRNA
- microRNA
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Affiliation(s)
- Petr V Nazarov
- Multiomics Data Science Research Group, Department of Oncology & Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Strassen L-1445, Luxembourg
| | - Stephanie Kreis
- Signal Transduction Group, Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
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Morenikeji OB, Wallace M, Strutton E, Bernard K, Yip E, Thomas BN. Integrative Network Analysis of Predicted miRNA-Targets Regulating Expression of Immune Response Genes in Bovine Coronavirus Infection. Front Genet 2020; 11:584392. [PMID: 33193717 PMCID: PMC7554596 DOI: 10.3389/fgene.2020.584392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Bovine coronavirus (BCoV) infection that causes disease outbreaks among farm animals, resulting in significant economic losses particularly in the cattle industry, has the potential to become zoonotic. miRNAs, which are short non-coding segments of RNA that inhibits the expression of their target genes, have been identified as potential biomarkers and drug targets, though this potential in BCoV remains largely unknown. We hypothesize that certain miRNAs could simultaneously target multiple genes, are significantly conserved across many species, thereby demonstrating the potential to serve as diagnostic or therapeutic tools for bovine coronavirus infection. To this end, we utilized different existing and publicly available computational tools to conduct system analysis predicting important miRNAs that could affect BCoV pathogenesis. Eleven genes including CEBPD, IRF1, TLR9, SRC, and RHOA, significantly indicated in immune-related pathways, were identified to be associated with BCoV, and implicated in other coronaviruses. Of the 70 miRNAs predicted to target the identified genes, four concomitant miRNAs (bta-miR-11975, bta-miR-11976, bta-miR-22-3p, and bta-miR-2325c) were found. Examining the gene interaction network suggests IL-6, IRF1, and TP53 as key drivers. Phylogenetic analysis revealed that miR-22 was completely conserved across all 14 species it was searched against, suggesting a shared and important functional role. Functional annotation and associated pathways of target genes, such as positive regulation of cytokine production, IL-6 signaling pathway, and regulation of leukocyte differentiation, indicate the miRNAs are major participants in multiple aspects of both innate and adaptive immune response. Examination of variants evinced a potentially deleterious SNP in bta-miR-22-3p and an advantageous SNP in bta-miR-2325c. Conclusively, this study provides new insight into miRNAs regulating genes responding to BCoV infection, with bta-miR-22-3p particularly indicated as a potential drug target or diagnostic marker for bovine coronavirus.
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Affiliation(s)
| | | | - Ellis Strutton
- Department of Biology, Hamilton College, Clinton, NY, United States
| | - Kahleel Bernard
- Department of Biology, Hamilton College, Clinton, NY, United States
| | - Elaine Yip
- Department of Biology, Hamilton College, Clinton, NY, United States
| | - Bolaji N Thomas
- Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY, United States
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Wu TR, Yin MM, Jiao CN, Gao YL, Kong XZ, Liu JX. MCCMF: collaborative matrix factorization based on matrix completion for predicting miRNA-disease associations. BMC Bioinformatics 2020; 21:454. [PMID: 33054708 PMCID: PMC7556955 DOI: 10.1186/s12859-020-03799-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023] Open
Abstract
Background MicroRNAs (miRNAs) are non-coding RNAs with regulatory functions. Many studies have shown that miRNAs are closely associated with human diseases. Among the methods to explore the relationship between the miRNA and the disease, traditional methods are time-consuming and the accuracy needs to be improved. In view of the shortcoming of previous models, a method, collaborative matrix factorization based on matrix completion (MCCMF) is proposed to predict the unknown miRNA-disease associations. Results The complete matrix of the miRNA and the disease is obtained by matrix completion. Moreover, Gaussian Interaction Profile kernel is added to the miRNA functional similarity matrix and the disease semantic similarity matrix. Then the Weight K Nearest Known Neighbors method is used to pretreat the association matrix, so the model is close to the reality. Finally, collaborative matrix factorization method is applied to obtain the prediction results. Therefore, the MCCMF obtains a satisfactory result in the fivefold cross-validation, with an AUC of 0.9569 (0.0005). Conclusions The AUC value of MCCMF is higher than other advanced methods in the fivefold cross validation experiment. In order to comprehensively evaluate the performance of MCCMF, accuracy, precision, recall and f-measure are also added. The final experimental results demonstrate that MCCMF outperforms other methods in predicting miRNA-disease associations. In the end, the effectiveness and practicability of MCCMF are further verified by researching three specific diseases.
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Affiliation(s)
- Tian-Ru Wu
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Meng-Meng Yin
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Cui-Na Jiao
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Ying-Lian Gao
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Xiang-Zhen Kong
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China
| | - Jin-Xing Liu
- School of Computer Science, Qufu Normal University, Rizhao, 276826, China.
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Tang L, Li P, Li L. Whole transcriptome expression profiles in placenta samples from women with gestational diabetes mellitus. J Diabetes Investig 2020; 11:1307-1317. [PMID: 32174045 PMCID: PMC7477506 DOI: 10.1111/jdi.13250] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 01/27/2020] [Accepted: 02/16/2020] [Indexed: 01/04/2023] Open
Abstract
AIMS/INTRODUCTION Non-coding ribonucleic acids (ncRNAs) have recently been shown to be involved in various biological processes. However, most of these ncRNAs are of unknown function or without annotation. This study first investigated the whole transcriptome profiles of placentas to identify the potential functions that ncRNAs exerted in gestational diabetes mellitus (GDM). MATERIALS AND METHODS Six placenta samples from healthy pregnant women (n = 3) and GDM (n = 3) were collected to analyze the whole transcriptome profiles by high-throughput sequencing. Differentially expressed ncRNAs were further validated by quantitative real-time polymerase chain reaction on an independent set of normal (n = 20) and GDM (n = 20) placenta samples. RESULTS A total of 2,817 microRNAs (miRNAs), 23,339 long non-coding RNAs (lncRNAs) and 9,513 circular RNAs (circRNAs) were identified. There were 290 differentially expressed ncRNAs in GDM placentas compared with the placentas of healthy pregnant women. Two miRNAs, 86 lncRNAs and 55 circRNAs were upregulated, while two miRNAs, 86 lncRNAs and 59 circRNAs were downregulated in GDM. The expression of the selected ncRNAs, which were further validated by quantitative real-time polymerase chain reaction, was consistent with the sequencing results. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the major targets of these ncRNAs were associated with insulin resistance, and abnormal glucose and lipid metabolism. A GDM-related competing endogenous RNA network suggested the interactions between lncRNAs, circRNAs, messenger RNAs and miRNAs. CONCLUSIONS The whole transcriptome profiles significantly differed in GDM placentas compared with the placentas of healthy pregnant women, which might be valuable for detecting novel ncRNAs, and providing new research insights into exploring the pathogenic mechanisms of GDM.
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Affiliation(s)
- Lei Tang
- Department of EndocrinologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Ping Li
- Department of EndocrinologyShengjing Hospital of China Medical UniversityShenyangChina
| | - Ling Li
- Department of EndocrinologyShengjing Hospital of China Medical UniversityShenyangChina
- Liaoning Province Key Laboratory of Endocrine DiseasesShenyangChina
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12
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Drug repositioning based on the target microRNAs using bilateral-inductive matrix completion. Mol Genet Genomics 2020; 295:1305-1314. [DOI: 10.1007/s00438-020-01702-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022]
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13
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Chen H, Guo R, Li G, Zhang W, Zhang Z. Comparative analysis of similarity measurements in miRNAs with applications to miRNA-disease association predictions. BMC Bioinformatics 2020; 21:176. [PMID: 32366225 PMCID: PMC7199309 DOI: 10.1186/s12859-020-3515-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND As regulators of gene expression, microRNAs (miRNAs) are increasingly recognized as critical biomarkers of human diseases. Till now, a series of computational methods have been proposed to predict new miRNA-disease associations based on similarity measurements. Different categories of features in miRNAs are applied in these methods for miRNA-miRNA similarity calculation. Benchmarking tests on these miRNA similarity measures are warranted to assess their effectiveness and robustness. RESULTS In this study, 5 categories of features, i.e. miRNA sequences, miRNA expression profiles in cell-lines, miRNA expression profiles in tissues, gene ontology (GO) annotations of miRNA target genes and Medical Subject Heading (MeSH) terms of miRNA-associated diseases, are collected and similarity values between miRNAs are quantified based on these feature spaces, respectively. We systematically compare the 5 similarities from multi-statistical views. Furthermore, we adopt a rule-based inference method to test their performance on miRNA-disease association predictions with the similarity measurements. Comprehensive comparison is made based on leave-one-out cross-validations and a case study. Experimental results demonstrate that the similarity measurement using MeSH terms performs best among the 5 measurements. It should be noted that the other 4 measurements can also achieve reliable prediction performance. The best-performed similarity measurement is used for new miRNA-disease association predictions and the inferred results are released for further biomedical screening. CONCLUSIONS Our study suggests that all the 5 features, even though some are restricted by data availability, are useful information for inferring novel miRNA-disease associations. However, biased prediction results might be produced in GO- and MeSH-based similarity measurements due to incomplete feature spaces. Similarity fusion may help produce more reliable prediction results. We expect that future studies will provide more detailed information into the 5 feature spaces and widen our understanding about disease pathogenesis.
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Affiliation(s)
- Hailin Chen
- School of Software, East China Jiaotong University, Nanchang, 330013 China
| | - Ruiyu Guo
- School of Software, East China Jiaotong University, Nanchang, 330013 China
| | - Guanghui Li
- School of Information Engineering, East China Jiaotong University, Nanchang, 330013 China
| | - Wei Zhang
- School of Science, East China Jiaotong University, Nanchang, 330013 China
| | - Zuping Zhang
- School of Computer Science and Engineering, Central South University, Changsha, 410083 China
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14
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Canonical Correlation Study on the Relationship between Shipping Development and Water Environment of the Yangtze River. SUSTAINABILITY 2020. [DOI: 10.3390/su12083279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The sustainable development of the Yangtze River will affect the lives of the people who live along it as well as the development of cities beside it. This study investigated the relationship between shipping development and the water environment of the Yangtze River. Canonical correlation analysis is a multivariate statistical method used to study the correlation between two groups of variables; this study employed it to analyze data relevant to shipping and the water environment of the Yangtze River from 2006 to 2016. Furthermore, the Yangtze River Shipping Prosperity Index and Yangtze River mainline freight volume were used to characterize the development of Yangtze River shipping. The water environment of the Yangtze River is characterized by wastewater discharge, ammonia nitrogen concentration, biochemical oxygen demand, the potassium permanganate index, and petroleum pollution. The results showed that a significant correlation exists between Yangtze River shipping and the river’s water environment. Furthermore, mainline freight volume has a significant impact on the quantity of wastewater discharged and petroleum pollution in the water environment.
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