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BMC Genomics. 2018 Nov 26;19(1):839. doi: 10.1186/s12864-018-5227-3.

Prediction of plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models.

Author information

1
Sino-Dutch Biomedical and Information Engineering School, Northeastern University, Shenyang, 110169, Liaoning, China.
2
Light Industry College, Liaoning University, Shenyang, 110036, Liaoning, China.
3
Department of Network Engineering, Zhengzhou Science and Technology Institute, Zhengzhou, 450000, Henan, China.
4
School of Life Science and Medicine, Dalian University of Technology, Panjin, 124221, China.
5
Department of Nuclear Medicine, The General Hospital of Shenyang Military Area Command, Shenyang, 110840, China.
6
Computer Science and Technology College, Jilin University, Changchun, 130012, China.
7
Bio-, Electro- And Mechanical Systems, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50 CP165/56, 1050, Brussels, Belgium. xiaoya.fan@ulb.ac.be.

Abstract

BACKGROUND:

An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective absorption of plant-derived xenomiRs by animals.

RESULTS:

Here, we analyzed 166 plant-derived xenomiRs reported in our previous study and 942 non-xenomiRs extracted from miRNA expression profiles of four species of commonly consumed plants. Employing statistics analysis and cluster analysis, our study revealed the potential sequence specificity of plant-derived xenomiRs. Furthermore, a random forest model and a one-dimensional convolutional neural network model were trained using miRNA sequence features and raw miRNA sequences respectively and then employed to predict unlabeled plant miRNAs in miRBase. A total of 241 possible plant-derived xenomiRs were predicted by both models. Finally, the potential functions of these possible plant-derived xenomiRs along with our previously reported ones in human body were analyzed.

CONCLUSIONS:

Our study, for the first time, presents the systematic plant-derived xenomiR sequences analysis and provides evidence for selective absorption of plant miRNA by human body, which could facilitate the future investigation about the mechanisms underlying the transference of plant-derived xenomiR.

KEYWORDS:

Cross-kingdom regulation; Machine learning; Plant-derived xenomiR; Selective absorption; Statistics analysis; miRNA

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