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Zhang ZY, Ning L, Ye X, Yang YH, Futamura Y, Sakurai T, Lin H. iLoc-miRNA: extracellular/intracellular miRNA prediction using deep BiLSTM with attention mechanism. Brief Bioinform 2022; 23:6693601. [PMID: 36070864 DOI: 10.1093/bib/bbac395] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/27/2022] [Accepted: 08/13/2022] [Indexed: 11/13/2022] Open
Abstract
The location of microRNAs (miRNAs) in cells determines their function in regulation activity. Studies have shown that miRNAs are stable in the extracellular environment that mediates cell-to-cell communication and are located in the intracellular region that responds to cellular stress and environmental stimuli. Though in situ detection techniques of miRNAs have made great contributions to the study of the localization and distribution of miRNAs, miRNA subcellular localization and their role are still in progress. Recently, some machine learning-based algorithms have been designed for miRNA subcellular location prediction, but their performance is still far from satisfactory. Here, we present a new data partitioning strategy that categorizes functionally similar locations for the precise and instructive prediction of miRNA subcellular location in Homo sapiens. To characterize the localization signals, we adopted one-hot encoding with post padding to represent the whole miRNA sequences, and proposed a deep bidirectional long short-term memory with the multi-head self-attention algorithm to model. The algorithm showed high selectivity in distinguishing extracellular miRNAs from intracellular miRNAs. Moreover, a series of motif analyses were performed to explore the mechanism of miRNA subcellular localization. To improve the convenience of the model, a user-friendly web server named iLoc-miRNA was established (http://iLoc-miRNA.lin-group.cn/).
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Affiliation(s)
- Zhao-Yue Zhang
- Tsukuba Life Science Innovation Program, University of Tsukuba, Tsukuba 3058577, Japan
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, 611844, Chengdu, China
| | - Xiucai Ye
- Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan
| | - Yu-He Yang
- Center for Information Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yasunori Futamura
- Tsukuba Life Science Innovation Program, University of Tsukuba, Tsukuba 3058577, Japan.,Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan
| | - Tetsuya Sakurai
- Tsukuba Life Science Innovation Program, University of Tsukuba, Tsukuba 3058577, Japan.,Department of Computer Science, University of Tsukuba, Tsukuba 3058577, Japan
| | - Hao Lin
- Center for Information Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Feng C, Cui L, Jin Z, Sun L, Wang X, Chi X, Sun Q, Lian S. Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma. BMC Genom Data 2022; 23:10. [PMID: 35123404 PMCID: PMC8818217 DOI: 10.1186/s12863-022-01028-y] [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: 06/24/2021] [Accepted: 01/19/2022] [Indexed: 12/24/2022] Open
Abstract
Background Endometrial carcinoma (EC) is one of the most common gynecological malignant tumors. In this study, we constructed gene co-expression networks to identify key modules and hub genes involved in the pathogenesis of EC. Results The MEturquoise module was found to be significantly related to hypertension and the MEbrown module was significantly related to the history of other malignancies. Functional enrichment analysis showed that the MEturquoise module was associated with the GO biological process terms of transcription from RNA polymerase II promoter, positive regulation of male gonad development, endocardial cushion development, and endothelial cell differentiation. The MEbrown module was associated with GO terms DNA binding, epithelial-to-mesenchymal transition, and transcription from RNA polymerase II promoter. A total of 10 hub genes were identified and compared with the available datasets at transcriptional and translational levels. Conclusions The identified ceRNAs may play a critical role in the progression and metastasis of EC and are thus candidate therapeutic targets and potential prognostic biomarkers. The two modules constructed further provide a useful reference that will advance understanding of the mechanisms of tumorigenesis in EC. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01028-y.
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Affiliation(s)
- Chong Feng
- Shengjing hospital affiliated to China medical university, No.36 ,Sanhao street, Heping district, Shenyang, Liaoning province, China
| | - Lei Cui
- School of health management, China medical university, No. 77, Puhe road, Shenbei new district, Shenyang, Liaoning province, China.
| | - Zhen Jin
- Shengjing hospital affiliated to China medical university, No.36 ,Sanhao street, Heping district, Shenyang, Liaoning province, China
| | - Lei Sun
- Shengjing hospital affiliated to China medical university, No.36 ,Sanhao street, Heping district, Shenyang, Liaoning province, China
| | - Xiaoyan Wang
- Shengjing hospital affiliated to China medical university, No.36 ,Sanhao street, Heping district, Shenyang, Liaoning province, China
| | - Xinshu Chi
- Shengjing hospital affiliated to China medical university, No.36 ,Sanhao street, Heping district, Shenyang, Liaoning province, China
| | - Qian Sun
- Shengjing hospital affiliated to China medical university, No.36 ,Sanhao street, Heping district, Shenyang, Liaoning province, China
| | - Siyu Lian
- Shengjing hospital affiliated to China medical university, No.36 ,Sanhao street, Heping district, Shenyang, Liaoning province, China
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