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. 2019 Apr 5;13(Suppl 2):26.
doi: 10.1186/s12918-019-0696-9.

FCMDAP: using miRNA family and cluster information to improve the prediction accuracy of disease related miRNAs

Xiaoying Li  1 , Yaping Lin  1 , Changlong Gu  2 , Jialiang Yang  3
Affiliations

FCMDAP: using miRNA family and cluster information to improve the prediction accuracy of disease related miRNAs

Xiaoying Li et al. BMC Syst Biol. .

Abstract

Background: Biological experiments have confirmed the association between miRNAs and various diseases. However, such experiments are costly and time consuming. Computational methods help select potential disease-related miRNAs to improve the efficiency of biological experiments.

Methods: In this work, we develop a novel method using multiple types of data to calculate miRNA and disease similarity based on mutual information, and add miRNA family and cluster information to predict human disease-related miRNAs (FCMDAP). This method not only depends on known miRNA-diseases associations but also accurately measures miRNA and disease similarity and resolves the problem of overestimation. FCMDAP uses the k most similar neighbor recommendation algorithm to predict the association score between miRNA and disease. Information about miRNA cluster is also used to improve prediction accuracy.

Result: FCMDAP achieves an average AUC of 0.9165 based on leave-one-out cross validation. Results confirm the 100, 98 and 96% of the top 50 predicted miRNAs reported in case studies on colorectal, lung, and pancreatic neoplasms. FCMDAP also exhibits satisfactory performance in predicting diseases without any related miRNAs and miRNAs without any related diseases.

Conclusions: In this study, we present a computational method FCMDAP to improve the prediction accuracy of disease related miRNAs. FCMDAP could be an effective tool for further biological experiments.

Keywords: Disease-related miRNA; Leave-one-out cross validation; Nearest neighbor recommendation algorithm; miRNA cluster information; miRNA family information.

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Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
The flowchart of FCMDAP
Fig. 2
Fig. 2
The ROC curve and AUC value of FCMDAP and other compared methods
Fig. 3
Fig. 3
Average AUCs value affected by α, β
See this image and copyright information in PMC

References

    1. Bartel DP. MicroRNAs. Genomics, biogenesis, mechanism, and function. Cell. 2004;116(2):281–297. doi: 10.1016/S0092-8674(04)00045-5. - DOI - PubMed
    1. He L, Thomson JM, Hemann MT, Hernandomonge E, Mu D, Goodson S, Powers S, Cordoncardo C, Lowe SW, Hannon GJ. A microRNA polycistron as a potential human oncogene. Nature. 2005;435(7043):828–833. doi: 10.1038/nature03552. - DOI - PMC - PubMed
    1. Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H, Harano T, Yatabe Y, Nagino M, Nimura Y. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 2004;64(11):3753–3756. doi: 10.1158/0008-5472.CAN-04-0637. - DOI - PubMed
    1. Rosenfeld N, Aharonov R, Meiri E, Rosenwald S, Spector Y, Zepeniuk M, Benjamin H, Shabes N, Tabak S, Levy A, et al. MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol. 2008;26:462. doi: 10.1038/nbt1392. - DOI - PubMed
    1. Tang W, Wan S, Yang Z, Teschendorff AE, Zou Q. Tumor origin detection with tissue-specific miRNA and DNA methylation markers. Bioinformatics. 2018;34(3):398–406. doi: 10.1093/bioinformatics/btx622. - DOI - PubMed

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