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Lu H, Zhang J, Cao Y, Wu S, Wei Y, Yin R. Advances in applications of artificial intelligence algorithms for cancer-related miRNA research. Zhejiang Da Xue Xue Bao Yi Xue Ban 2024; 53:231-243. [PMID: 38650448 PMCID: PMC11057993 DOI: 10.3724/zdxbyxb-2023-0511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/30/2024] [Indexed: 04/25/2024]
Abstract
MiRNAs are a class of small non-coding RNAs, which regulate gene expression post-transcriptionally by partial complementary base pairing. Aberrant miRNA expressions have been reported in tumor tissues and peripheral blood of cancer patients. In recent years, artificial intelligence algorithms such as machine learning and deep learning have been widely used in bioinformatic research. Compared to traditional bioinformatic tools, miRNA target prediction tools based on artificial intelligence algorithms have higher accuracy, and can successfully predict subcellular localization and redistribution of miRNAs to deepen our understanding. Additionally, the construction of clinical models based on artificial intelligence algorithms could significantly improve the mining efficiency of miRNA used as biomarkers. In this article, we summarize recent development of bioinformatic miRNA tools based on artificial intelligence algorithms, focusing on the potential of machine learning and deep learning in cancer-related miRNA research.
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Affiliation(s)
- Hongyu Lu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China.
| | - Jia Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Yixin Cao
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Shuming Wu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China
| | - Yuan Wei
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China.
| | - Runting Yin
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China.
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2
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Emami N, Ferdousi R. HormoNet: a deep learning approach for hormone-drug interaction prediction. BMC Bioinformatics 2024; 25:87. [PMID: 38418979 PMCID: PMC10903040 DOI: 10.1186/s12859-024-05708-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Several experimental evidences have shown that the human endogenous hormones can interact with drugs in many ways and affect drug efficacy. The hormone drug interactions (HDI) are essential for drug treatment and precision medicine; therefore, it is essential to understand the hormone-drug associations. Here, we present HormoNet to predict the HDI pairs and their risk level by integrating features derived from hormone and drug target proteins. To the best of our knowledge, this is one of the first attempts to employ deep learning approach for prediction of HDI prediction. Amino acid composition and pseudo amino acid composition were applied to represent target information using 30 physicochemical and conformational properties of the proteins. To handle the imbalance problem in the data, we applied synthetic minority over-sampling technique technique. Additionally, we constructed novel datasets for HDI prediction and the risk level of their interaction. HormoNet achieved high performance on our constructed hormone-drug benchmark datasets. The results provide insights into the understanding of the relationship between hormone and a drug, and indicate the potential benefit of reducing risk levels of interactions in designing more effective therapies for patients in drug treatments. Our benchmark datasets and the source codes for HormoNet are available in: https://github.com/EmamiNeda/HormoNet .
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Affiliation(s)
- Neda Emami
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Reza Ferdousi
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Tabriz, Iran
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3
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Wang J, Horlacher M, Cheng L, Winther O. RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies. Brief Bioinform 2023; 24:bbad249. [PMID: 37466130 PMCID: PMC10516376 DOI: 10.1093/bib/bbad249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss RNA localization in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types of molecular mechanisms that control the localization of RNA to distinct cellular compartments are reviewed, including directed transport, protection from mRNA degradation, as well as diffusion and local entrapment. Advances in experimental methods, both image and sequence based, provide substantial data resources, which allow for the design of powerful machine learning models to predict RNA localizations. We review the publicly available predictive tools to serve as a guide for users and inspire developers to build more effective prediction models. Finally, we provide an overview of multimodal learning, which may provide a new avenue for the prediction of RNA localization.
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Affiliation(s)
- Jun Wang
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center, Munich, Germany
| | - Lixin Cheng
- Shenzhen People’s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China
| | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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4
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Temilola DO, Wium M, Paccez J, Salukazana AS, Otu HH, Carbone GM, Kaestner L, Cacciatore S, Zerbini LF. Potential of miRNAs in Plasma Extracellular Vesicle for the Stratification of Prostate Cancer in a South African Population. Cancers (Basel) 2023; 15:3968. [PMID: 37568783 PMCID: PMC10417259 DOI: 10.3390/cancers15153968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Prostate cancer (PCa) is the most common cause of cancer death among African men. The analysis of microRNAs (miRNAs) in plasma extracellular vesicles (EVs) can be utilized as a non-invasive tool for the diagnosis of PCa. In this study, we used small RNA sequencing to profile miRNAs cargo in plasma EVs from South African PCa patients. We evaluated the differential expression of miRNAs between low and high Gleason scores in the plasma EVs of South African patients and in the prostatic tissue from data available in the Cancer Genome Atlas (TCGA) Data Portal. We identified 7 miRNAs differently expressed in both EVs and prostatic tissues. We evaluated their expression using qPCR in a larger cohort of 10 patients with benign prostatic hyperplasia (BPH) and 24 patients with PCa. Here, we reported that the ratio between two of these miRNAs (i.e., miR-194-5p/miR-16-5p) showed a higher concentration in PCa compared to BPH and in metastatic PCa compared to localized PCa. We explored for the first time the profiling of miRNAs cargo in plasma EVs as a tool for the identification of putative markers in the South African population. Our finding indicated the ratio miR-194-5p/miR-16-5p as a non-invasive marker for the evaluation of PCa aggressiveness in this population.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
| | - Juliano Paccez
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
| | - Azola Samkele Salukazana
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town 7925, South Africa
| | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Giuseppina M. Carbone
- Institute of Oncology Research (IOR), Università della Svizzera italiana, 6900 Bellinzona, Switzerland
| | - Lisa Kaestner
- Division of Urology, University of Cape Town, Groote Schuur Hospital, Cape Town 7925, South Africa
| | - Stefano Cacciatore
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
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5
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Bai T, Yan K, Liu B. DAmiRLocGNet: miRNA subcellular localization prediction by combining miRNA-disease associations and graph convolutional networks. Brief Bioinform 2023:bbad212. [PMID: 37332057 DOI: 10.1093/bib/bbad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023] Open
Abstract
MicroRNAs (miRNAs) are human post-transcriptional regulators in humans, which are involved in regulating various physiological processes by regulating the gene expression. The subcellular localization of miRNAs plays a crucial role in the discovery of their biological functions. Although several computational methods based on miRNA functional similarity networks have been presented to identify the subcellular localization of miRNAs, it remains difficult for these approaches to effectively extract well-referenced miRNA functional representations due to insufficient miRNA-disease association representation and disease semantic representation. Currently, there has been a significant amount of research on miRNA-disease associations, making it possible to address the issue of insufficient miRNA functional representation. In this work, a novel model is established, named DAmiRLocGNet, based on graph convolutional network (GCN) and autoencoder (AE) for identifying the subcellular localizations of miRNA. The DAmiRLocGNet constructs the features based on miRNA sequence information, miRNA-disease association information and disease semantic information. GCN is utilized to gather the information of neighboring nodes and capture the implicit information of network structures from miRNA-disease association information and disease semantic information. AE is employed to capture sequence semantics from sequence similarity networks. The evaluation demonstrates that the performance of DAmiRLocGNet is superior to other competing computational approaches, benefiting from implicit features captured by using GCNs. The DAmiRLocGNet has the potential to be applied to the identification of subcellular localization of other non-coding RNAs. Moreover, it can facilitate further investigation into the functional mechanisms underlying miRNA localization. The source code and datasets are accessed at http://bliulab.net/DAmiRLocGNet.
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Affiliation(s)
- Tao Bai
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China
- School of Mathematics & Computer Science, Yan'an University, Shaanxi 716000, China
| | - Ke Yan
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China
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6
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Systematic analysis of different degrees of haemolysis on miRNA levels in serum and serum-derived extracellular vesicles from dogs. BMC Vet Res 2022; 18:355. [PMID: 36138476 PMCID: PMC9494854 DOI: 10.1186/s12917-022-03445-8] [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: 03/04/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Background Circulating microRNAs (miRNAs) are described as promising non-invasive biomarkers for diagnostics and therapeutics. Human studies have shown that haemolysis occurring during blood collection or due to improper sample processing/storage significantly alters the miRNA content in plasma and serum. Nevertheless, no similar research has been performed in dogs so far. We therefore investigated the effects of different degrees of haemolysis on the levels of selected miRNAs in serum and serum-derived extracellular vesicles (EVs) from dogs, by inducing a controlled in vitro haemolysis experiment. Results The abundance of miR-16, miR-92a, miR-191, miR-451 and miR-486 was significantly sensitive to haemolysis in serum and serum-derived EVs, while other selected miRNAs were not influenced by haemolysis. Furthermore, we found that the abundance of some canine miRNAs differs from data reported in the human system. Conclusions Our results describe for the first time the impact of haemolysis on circulating miRNAs not only in whole serum, but also in serum-derived EVs from dogs. Hence, we provide novel data for further analyses in the discovery of canine circulating biomarkers. Our findings suggest that haemolysis should be carefully assessed to assure accuracy when investigating circulating miRNA in serum or plasma-based tests. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03445-8.
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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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8
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Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Circ-LocNet: A Computational Framework for Circular RNA Sub-Cellular Localization Prediction. Int J Mol Sci 2022; 23:ijms23158221. [PMID: 35897818 PMCID: PMC9329987 DOI: 10.3390/ijms23158221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Circular ribonucleic acids (circRNAs) are novel non-coding RNAs that emanate from alternative splicing of precursor mRNA in reversed order across exons. Despite the abundant presence of circRNAs in human genes and their involvement in diverse physiological processes, the functionality of most circRNAs remains a mystery. Like other non-coding RNAs, sub-cellular localization knowledge of circRNAs has the aptitude to demystify the influence of circRNAs on protein synthesis, degradation, destination, their association with different diseases, and potential for drug development. To date, wet experimental approaches are being used to detect sub-cellular locations of circular RNAs. These approaches help to elucidate the role of circRNAs as protein scaffolds, RNA-binding protein (RBP) sponges, micro-RNA (miRNA) sponges, parental gene expression modifiers, alternative splicing regulators, and transcription regulators. To complement wet-lab experiments, considering the progress made by machine learning approaches for the determination of sub-cellular localization of other non-coding RNAs, the paper in hand develops a computational framework, Circ-LocNet, to precisely detect circRNA sub-cellular localization. Circ-LocNet performs comprehensive extrinsic evaluation of 7 residue frequency-based, residue order and frequency-based, and physio-chemical property-based sequence descriptors using the five most widely used machine learning classifiers. Further, it explores the performance impact of K-order sequence descriptor fusion where it ensembles similar as well dissimilar genres of statistical representation learning approaches to reap the combined benefits. Considering the diversity of statistical representation learning schemes, it assesses the performance of second-order, third-order, and going all the way up to seventh-order sequence descriptor fusion. A comprehensive empirical evaluation of Circ-LocNet over a newly developed benchmark dataset using different settings reveals that standalone residue frequency-based sequence descriptors and tree-based classifiers are more suitable to predict sub-cellular localization of circular RNAs. Further, K-order heterogeneous sequence descriptors fusion in combination with tree-based classifiers most accurately predict sub-cellular localization of circular RNAs. We anticipate this study will act as a rich baseline and push the development of robust computational methodologies for the accurate sub-cellular localization determination of novel circRNAs.
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Affiliation(s)
- Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
- Correspondence:
| | - Muhammad Ali Ibrahim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Imran Malik
- School of Computer Science & Electrical Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan;
| | - Andreas Dengel
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- DeepReader GmbH, Trippstadter Str. 122, 67663 Kaiserslautern, Germany
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9
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EL-RMLocNet: An Explainable LSTM Network for RNA-Associated Multi-Compartment Localization Prediction. Comput Struct Biotechnol J 2022; 20:3986-4002. [PMID: 35983235 PMCID: PMC9356161 DOI: 10.1016/j.csbj.2022.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/16/2022] [Accepted: 07/16/2022] [Indexed: 11/23/2022] Open
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10
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Xu M, Chen Y, Xu Z, Zhang L, Jiang H, Pian C. MiRLoc: predicting miRNA subcellular localization by incorporating miRNA-mRNA interactions and mRNA subcellular localization. Brief Bioinform 2022; 23:6532537. [PMID: 35183063 DOI: 10.1093/bib/bbac044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/17/2022] [Accepted: 01/28/2022] [Indexed: 12/19/2022] Open
Abstract
Subcellular localization of microRNAs (miRNAs) is an important reflection of their biological functions. Considering the spatio-temporal specificity of miRNA subcellular localization, experimental detection techniques are expensive and time-consuming, which strongly motivates an efficient and economical computational method to predict miRNA subcellular localization. In this paper, we describe a computational framework, MiRLoc, to predict the subcellular localization of miRNAs. In contrast to existing methods, MiRLoc uses the functional similarity between miRNAs instead of sequence features and incorporates information about the subcellular localization of the corresponding target mRNAs. The results show that miRNA functional similarity data can be effectively used to predict miRNA subcellular localization, and that inclusion of subcellular localization information of target mRNAs greatly improves prediction performance.
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Affiliation(s)
- Mingmin Xu
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yuanyuan Chen
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhihui Xu
- Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu, China
| | - Liangyun Zhang
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Hangjin Jiang
- Center for Data Science, Zhejiang University, Hangzhou, Zhejiang, China
| | - Cong Pian
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Simcere Diagnostics Co., Ltd., Nanjing, Jiangsu, China
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11
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Savulescu AF, Bouilhol E, Beaume N, Nikolski M. Prediction of RNA subcellular localization: Learning from heterogeneous data sources. iScience 2021; 24:103298. [PMID: 34765919 PMCID: PMC8571491 DOI: 10.1016/j.isci.2021.103298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RNA subcellular localization has recently emerged as a widespread phenomenon, which may apply to the majority of RNAs. The two main sources of data for characterization of RNA localization are sequence features and microscopy images, such as obtained from single-molecule fluorescent in situ hybridization-based techniques. Although such imaging data are ideal for characterization of RNA distribution, these techniques remain costly, time-consuming, and technically challenging. Given these limitations, imaging data exist only for a limited number of RNAs. We argue that the field of RNA localization would greatly benefit from complementary techniques able to characterize location of RNA. Here we discuss the importance of RNA localization and the current methodology in the field, followed by an introduction on prediction of location of molecules. We then suggest a machine learning approach based on the integration between imaging localization data and sequence-based data to assist in characterization of RNA localization on a transcriptome level.
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Affiliation(s)
- Anca Flavia Savulescu
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925 Cape Town, South Africa
| | - Emmanuel Bouilhol
- Université de Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Nicolas Beaume
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town,7925 Cape Town, South Africa
| | - Macha Nikolski
- Université de Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
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12
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Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs. Int J Mol Sci 2021; 22:8719. [PMID: 34445436 PMCID: PMC8395733 DOI: 10.3390/ijms22168719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Apart from protein-coding Ribonucleic acids (RNAs), there exists a variety of non-coding RNAs (ncRNAs) which regulate complex cellular and molecular processes. High-throughput sequencing technologies and bioinformatics approaches have largely promoted the exploration of ncRNAs which revealed their crucial roles in gene regulation, miRNA binding, protein interactions, and splicing. Furthermore, ncRNAs are involved in the development of complicated diseases like cancer. Categorization of ncRNAs is essential to understand the mechanisms of diseases and to develop effective treatments. Sub-cellular localization information of ncRNAs demystifies diverse functionalities of ncRNAs. To date, several computational methodologies have been proposed to precisely identify the class as well as sub-cellular localization patterns of RNAs). This paper discusses different types of ncRNAs, reviews computational approaches proposed in the last 10 years to distinguish coding-RNA from ncRNA, to identify sub-types of ncRNAs such as piwi-associated RNA, micro RNA, long ncRNA, and circular RNA, and to determine sub-cellular localization of distinct ncRNAs and RNAs. Furthermore, it summarizes diverse ncRNA classification and sub-cellular localization determination datasets along with benchmark performance to aid the development and evaluation of novel computational methodologies. It identifies research gaps, heterogeneity, and challenges in the development of computational approaches for RNA sequence analysis. We consider that our expert analysis will assist Artificial Intelligence researchers with knowing state-of-the-art performance, model selection for various tasks on one platform, dominantly used sequence descriptors, neural architectures, and interpreting inter-species and intra-species performance deviation.
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Affiliation(s)
- Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Ali Ibrahim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Imran Malik
- National Center for Artificial Intelligence (NCAI), National University of Sciences and Technology, Islamabad 44000, Pakistan;
- School of Electrical Engineering & Computer Science, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Andreas Dengel
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- DeepReader GmbH, Trippstadter Str. 122, 67663 Kaiserslautern, Germany
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