1
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Abnoosian K, Farnoosh R, Behzadi MH. Prediction of diabetes disease using an ensemble of machine learning multi-classifier models. BMC Bioinformatics 2023; 24:337. [PMID: 37697283 PMCID: PMC10496262 DOI: 10.1186/s12859-023-05465-z] [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: 03/30/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Diabetes is a life-threatening chronic disease with a growing global prevalence, necessitating early diagnosis and treatment to prevent severe complications. Machine learning has emerged as a promising approach for diabetes diagnosis, but challenges such as limited labeled data, frequent missing values, and dataset imbalance hinder the development of accurate prediction models. Therefore, a novel framework is required to address these challenges and improve performance. METHODS In this study, we propose an innovative pipeline-based multi-classification framework to predict diabetes in three classes: diabetic, non-diabetic, and prediabetes, using the imbalanced Iraqi Patient Dataset of Diabetes. Our framework incorporates various pre-processing techniques, including duplicate sample removal, attribute conversion, missing value imputation, data normalization and standardization, feature selection, and k-fold cross-validation. Furthermore, we implement multiple machine learning models, such as k-NN, SVM, DT, RF, AdaBoost, and GNB, and introduce a weighted ensemble approach based on the Area Under the Receiver Operating Characteristic Curve (AUC) to address dataset imbalance. Performance optimization is achieved through grid search and Bayesian optimization for hyper-parameter tuning. RESULTS Our proposed model outperforms other machine learning models, including k-NN, SVM, DT, RF, AdaBoost, and GNB, in predicting diabetes. The model achieves high average accuracy, precision, recall, F1-score, and AUC values of 0.9887, 0.9861, 0.9792, 0.9851, and 0.999, respectively. CONCLUSION Our pipeline-based multi-classification framework demonstrates promising results in accurately predicting diabetes using an imbalanced dataset of Iraqi diabetic patients. The proposed framework addresses the challenges associated with limited labeled data, missing values, and dataset imbalance, leading to improved prediction performance. This study highlights the potential of machine learning techniques in diabetes diagnosis and management, and the proposed framework can serve as a valuable tool for accurate prediction and improved patient care. Further research can build upon our work to refine and optimize the framework and explore its applicability in diverse datasets and populations.
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Affiliation(s)
- Karlo Abnoosian
- Department of Statistics, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rahman Farnoosh
- School of Mathematics, Iran University of Science and Technology, Tehran, Iran.
| | - Mohammad Hassan Behzadi
- Department of Statistics, Science and Research Branch, Islamic Azad University, Tehran, Iran
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2
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Pradhan UK, Meher PK, Naha S, Rao AR, Kumar U, Pal S, Gupta A. ASmiR: a machine learning framework for prediction of abiotic stress-specific miRNAs in plants. Funct Integr Genomics 2023; 23:92. [PMID: 36939943 DOI: 10.1007/s10142-023-01014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 03/21/2023]
Abstract
Abiotic stresses have become a major challenge in recent years due to their pervasive nature and shocking impacts on plant growth, development, and quality. MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of specific abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational model for prediction of miRNAs associated with four specific abiotic stresses such as cold, drought, heat and salt. The pseudo K-tuple nucleotide compositional features of Kmer size 1 to 5 were used to represent miRNAs in numeric form. Feature selection strategy was employed to select important features. With the selected feature sets, support vector machine (SVM) achieved the highest cross-validation accuracy in all four abiotic stress conditions. The highest cross-validated prediction accuracies in terms of area under precision-recall curve were found to be 90.15, 90.09, 87.71, and 89.25% for cold, drought, heat and salt respectively. Overall prediction accuracies for the independent dataset were respectively observed 84.57, 80.62, 80.38 and 82.78%, for the abiotic stresses. The SVM was also seen to outperform different deep learning models for prediction of abiotic stress-responsive miRNAs. To implement our method with ease, an online prediction server "ASmiR" has been established at https://iasri-sg.icar.gov.in/asmir/ . The proposed computational model and the developed prediction tool are believed to supplement the existing effort for identification of specific abiotic stress-responsive miRNAs in plants.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India.
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | | | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Soumen Pal
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
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3
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Su W, Xie XQ, Liu XW, Gao D, Ma CY, Zulfiqar H, Yang H, Lin H, Yu XL, Li YW. iRNA-ac4C: A novel computational method for effectively detecting N4-acetylcytidine sites in human mRNA. Int J Biol Macromol 2023; 227:1174-1181. [PMID: 36470433 DOI: 10.1016/j.ijbiomac.2022.11.299] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/10/2022] [Accepted: 11/25/2022] [Indexed: 12/07/2022]
Abstract
RNA N4-acetylcytidine (ac4C) is the acetylation of cytidine at the nitrogen-4 position, which is a highly conserved RNA modification and involves a variety of biological processes. Hence, accurate identification of genome-wide ac4C sites is vital for understanding regulation mechanism of gene expression. In this work, a novel predictor, named iRNA-ac4C, was established to identify ac4C sites in human mRNA based on three feature extraction methods, including nucleotide composition, nucleotide chemical property, and accumulated nucleotide frequency. Subsequently, minimum-Redundancy-Maximum-Relevance combined with incremental feature selection strategies was utilized to select the optimal feature subset. According to the optimal feature subset, the best ac4C classification model was trained by gradient boosting decision tree with 10-fold cross-validation. The results of independent testing set indicated that our proposed method could produce encouraging generalization capabilities. For the convenience of other researchers, we established a user-friendly web server which is freely available at http://lin-group.cn/server/iRNA-ac4C/. We hope that the tool could provide guide for wet-experimental scholars.
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Affiliation(s)
- Wei Su
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Xue-Qin Xie
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Xiao-Wei Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Dong Gao
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Cai-Yi Ma
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Hasan Zulfiqar
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Hui Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Hao Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Xiao-Long Yu
- School of Materials Science and Engineering, Hainan University, Haikou 570228, China.
| | - Yan-Wen Li
- School of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Key Laboratory of Intelligent Information Processing of Jilin Province, Northeast Normal University, Changchun 130117, China; Institute of Computational Biology, Northeast Normal University, Changchun 130117, China.
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4
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Identification of D Modification Sites Using a Random Forest Model Based on Nucleotide Chemical Properties. Int J Mol Sci 2022; 23:ijms23063044. [PMID: 35328461 PMCID: PMC8950657 DOI: 10.3390/ijms23063044] [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: 02/08/2022] [Revised: 02/25/2022] [Accepted: 03/09/2022] [Indexed: 12/03/2022] Open
Abstract
Dihydrouridine (D) is an abundant post-transcriptional modification present in transfer RNA from eukaryotes, bacteria, and archaea. D has contributed to treatments for cancerous diseases. Therefore, the precise detection of D modification sites can enable further understanding of its functional roles. Traditional experimental techniques to identify D are laborious and time-consuming. In addition, there are few computational tools for such analysis. In this study, we utilized eleven sequence-derived feature extraction methods and implemented five popular machine algorithms to identify an optimal model. During data preprocessing, data were partitioned for training and testing. Oversampling was also adopted to reduce the effect of the imbalance between positive and negative samples. The best-performing model was obtained through a combination of random forest and nucleotide chemical property modeling. The optimized model presented high sensitivity and specificity values of 0.9688 and 0.9706 in independent tests, respectively. Our proposed model surpassed published tools in independent tests. Furthermore, a series of validations across several aspects was conducted in order to demonstrate the robustness and reliability of our model.
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Clauwaert J, Waegeman W. Novel Transformer Networks for Improved Sequence Labeling in genomics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:97-106. [PMID: 33125335 DOI: 10.1109/tcbb.2020.3035021] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In genomics, a wide range of machine learning methodologies have been investigated to annotate biological sequences for positions of interest such as transcription start sites, translation initiation sites, methylation sites, splice sites and promoter start sites. In recent years, this area has been dominated by convolutional neural networks, which typically outperform previously-designed methods as a result of automated scanning for influential sequence motifs. However, those architectures do not allow for the efficient processing of the full genomic sequence. As an improvement, we introduce transformer architectures for whole genome sequence labeling tasks. We show that these architectures, recently introduced for natural language processing, are better suited for processing and annotating long DNA sequences. We apply existing networks and introduce an optimized method for the calculation of attention from input nucleotides. To demonstrate this, we evaluate our architecture on several sequence labeling tasks, and find it to achieve state-of-the-art performances when comparing it to specialized models for the annotation of transcription start sites, translation initiation sites and 4mC methylation in E. coli.
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6
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Fan Y, Wang W. Using multi-layer perceptron to identify origins of replication in eukaryotes via informative features. BMC Bioinformatics 2021; 22:516. [PMID: 34688247 PMCID: PMC8542328 DOI: 10.1186/s12859-021-04431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The origin is the starting site of DNA replication, an extremely vital part of the informational inheritance between parents and children. More importantly, accurately identifying the origin of replication has great application value in the diagnosis and treatment of diseases related to genetic information errors, while the traditional biological experimental methods are time-consuming and laborious. RESULTS We carried out research on the origin of replication in a variety of eukaryotes and proposed a unique prediction method for each species. Throughout the experiment, we collected data from 7 species, including Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, Kluyveromyces lactis, Pichia pastoris and Schizosaccharomyces pombe. In addition to the commonly used sequence feature extraction methods PseKNC-II and Base-content, we designed a feature extraction method based on TF-IDF. Then the two-step method was utilized for feature selection. After comparing a variety of traditional machine learning classification models, the multi-layer perceptron was employed as the classification algorithm. Ultimately, the data and codes involved in the experiment are available at https://github.com/Sarahyouzi/EukOriginPredict . CONCLUSIONS The prediction accuracy of the training set of the above-mentioned seven species after 100 times fivefold cross validation reach 92.60%, 90.80%, 91.22%, 96.15%, 96.72%, 99.86%, 96.72%, respectively. It denotes that compared with other methods, the methods we designed could accomplish superior performance. In addition, our experiments reveals that the models of multiple species could predict each other with high accuracy, and the results of STREME shows that they have a certain common motif.
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Affiliation(s)
- Yongxian Fan
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China.
| | - Wanru Wang
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China
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7
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Nosrati M, Amani J. In silico screening of ssDNA aptamer against Escherichia coli O157:H7: A machine learning and the Pseudo K-tuple nucleotide composition based approach. Comput Biol Chem 2021; 95:107568. [PMID: 34543910 DOI: 10.1016/j.compbiolchem.2021.107568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023]
Abstract
This study was planned to in silico screening of ssDNA aptamer against Escherichia coli O157:H7 by combination of machine learning and the PseKNC approach. For this, firstly a total numbers of 47 validated ssDNA aptamers as well as 498 random DNA sequences were considered as positive and negative training data respectively. The sequences then converted to numerical vectors using PseKNC method through Pse-in-one 2.0 web server. After that, the numerical vectors were subjected to classification by the SVM, ANN and RF algorithms available in Orange 3.2.0 software. The performances of the tested models were evaluated using cross-validation, random sampling and ROC curve analyzes. The primary results demonstrated that the ANN and RF algorithms have appropriate performances for the data classification. To improve the performances of mentioned classifiers the positive training data was triplicated and re-training process was also performed. The results confirmed that data size improvement had significant effect on the accuracy of data classification especially about RF model. Subsequently, the RF algorithm with accuracy of 98% was selected for aptamer screening. The thermodynamics details of folding process as well as secondary structures of the screened aptamers were also considered as final evaluations. The results confirmed that the selected aptamers by the proposed method had appropriate structure properties and there is no thermodynamics limit for the aptamers folding.
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Affiliation(s)
- Mokhtar Nosrati
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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8
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Akmal MA, Hussain W, Rasool N, Khan YD, Khan SA, Chou KC. Using CHOU'S 5-Steps Rule to Predict O-Linked Serine Glycosylation Sites by Blending Position Relative Features and Statistical Moment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2045-2056. [PMID: 31985438 DOI: 10.1109/tcbb.2020.2968441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Glycosylation of proteins in eukaryote cells is an important and complicated post-translation modification due to its pivotal role and association with crucial physiological functions within most of the proteins. Identification of glycosylation sites in a polypeptide chain is not an easy task due to multiple impediments. Analytical identification of these sites is expensive and laborious. There is a dire need to develop a reliable computational method for precise determination of such sites which can help researchers to save time and effort. Herein, we propose a novel predictor namely iGlycoS-PseAAC by integrating the Chou's Pseudo Amino Acid Composition (PseAAC) and relative/absolute position-based features. The self-consistency results show that the accuracy revealed by the model using the benchmark dataset for prediction of O-linked glycosylation having serine sites is 98.8 percent. The overall accuracy of predictor achieved through 10-fold cross validation by combining the positive and negative results is 97.2 percent. The overall accuracy achieved through Jackknife test is 96.195 percent by aggregating of all the prediction results. Thus the proposed predictor can help in predicting the O-linked glycosylated serine sites in an efficient and accurate way. The overall results show that the accuracy of the iGlycoS-PseAAC is higher than the existing tools.
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9
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Feng P, Feng L, Tang C. Comparison and Analysis of Computational Methods for Identifying N6-Methyladenosine Sites in Saccharomyces cerevisiae. Curr Pharm Des 2021; 27:1219-1229. [PMID: 33167827 DOI: 10.2174/1381612826666201109110703] [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: 05/09/2020] [Accepted: 07/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND N6-methyladenosine (m6A) plays critical roles in a broad range of biological processes. Knowledge about the precise location of m6A site in the transcriptome is vital for deciphering its biological functions. Although experimental techniques have made substantial contributions to identify m6A, they are still labor intensive and time consuming. As complement to experimental methods, in the past few years, a series of computational approaches have been proposed to identify m6A sites. METHODS In order to facilitate researchers to select appropriate methods for identifying m6A sites, it is necessary to conduct a comprehensive review and comparison of existing methods. RESULTS Since research works on m6A in Saccharomyces cerevisiae are relatively clear, in this review, we summarized recent progress of computational prediction of m6A sites in S. cerevisiae and assessed the performance of existing computational methods. Finally, future directions of computationally identifying m6A sites are presented. CONCLUSION Taken together, we anticipate that this review will serve as an important guide for computational analysis of m6A modifications.
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Affiliation(s)
- Pengmian Feng
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Lijing Feng
- School of Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Chaohui Tang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
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10
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Wang M, Xie J, Xu S. M6A-BiNP: predicting N 6-methyladenosine sites based on bidirectional position-specific propensities of polynucleotides and pointwise joint mutual information. RNA Biol 2021; 18:2498-2512. [PMID: 34161188 PMCID: PMC8632114 DOI: 10.1080/15476286.2021.1930729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) plays an important role in various biological processes. Identifying m6A site is a key step in exploring its biological functions. One of the biggest challenges in identifying m6A sites is how to extract features comprising rich categorical information to distinguish m6A and non-m6A sites. To address this challenge, we propose bidirectional dinucleotide and trinucleotide position-specific propensities, respectively, in this paper. Based on this, we propose two feature-encoding algorithms: Position-Specific Propensities and Pointwise Mutual Information (PSP-PMI) and Position-Specific Propensities and Pointwise Joint Mutual Information (PSP-PJMI). PSP-PMI is based on the bidirectional dinucleotide propensity and the pointwise mutual information, while PSP-PJMI is based on the bidirectional trinucleotide position-specific propensity and the proposed pointwise joint mutual information in this paper. We introduce parameters α and β in PSP-PMI and PSP-PJMI, respectively, to represent the distance from the nucleotide to its forward or backward adjacent nucleotide or dinucleotide, so as to extract features containing local and global classification information. Finally, we propose the M6A-BiNP predictor based on PSP-PMI or PSP-PJMI and SVM classifier. The 10-fold cross-validation experimental results on the benchmark datasets of non-single-base resolution and single-base resolution demonstrate that PSP-PMI and PSP-PJMI can extract features with strong capabilities to identify m6A and non-m6A sites. The M6A-BiNP predictor based on our proposed feature encoding algorithm PSP-PJMI is better than the state-of-the-art predictors, and it is so far the best model to identify m6A and non-m6A sites.
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Affiliation(s)
- Mingzhao Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Juanying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Shengquan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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Awais M, Hussain W, Khan YD, Rasool N, Khan SA, Chou KC. iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:596-610. [PMID: 31144645 DOI: 10.1109/tcbb.2019.2919025] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association, cytoskeletal dynamics, and enzymatic inhibition/activation. Phosphohistidine (PhosH) has a key role in a number of biological processes, including central metabolism to signalling in eukaryotes and bacteria. Thus, identification of phosphohistidine sites in a protein sequence is crucial, and experimental identification can be expensive, time-taking, and laborious. To address this problem, here, we propose a novel computational model namely iPhosH-PseAAC for prediction of phosphohistidine sites in a given protein sequence using pseudo amino acid composition (PseAAC), statistical moments, and position relative features. The results of the proposed predictor are validated through self-consistency testing, 10-fold cross-validation, and jackknife testing. The self-consistency validation gave the 100 percent accuracy, whereas, for cross-validation, the accuracy achieved is 94.26 percent. Moreover, jackknife testing gave 97.07 percent accuracy for the proposed model. Thus, the proposed model iPhosH-PseAAC for prediction of iPhosH site has the great ability to predict the PhosH sites in given proteins.
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Aziz AZB, Hasan MAM, Shin J. Identification of RNA pseudouridine sites using deep learning approaches. PLoS One 2021; 16:e0247511. [PMID: 33621235 PMCID: PMC7901771 DOI: 10.1371/journal.pone.0247511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/08/2021] [Indexed: 01/05/2023] Open
Abstract
Pseudouridine(Ψ) is widely popular among various RNA modifications which have been confirmed to occur in rRNA, mRNA, tRNA, and nuclear/nucleolar RNA. Hence, identifying them has vital significance in academic research, drug development and gene therapies. Several laboratory techniques for Ψ identification have been introduced over the years. Although these techniques produce satisfactory results, they are costly, time-consuming and requires skilled experience. As the lengths of RNA sequences are getting longer day by day, an efficient method for identifying pseudouridine sites using computational approaches is very important. In this paper, we proposed a multi-channel convolution neural network using binary encoding. We employed k-fold cross-validation and grid search to tune the hyperparameters. We evaluated its performance in the independent datasets and found promising results. The results proved that our method can be used to identify pseudouridine sites for associated purposes. We have also implemented an easily accessible web server at http://103.99.176.239/ipseumulticnn/.
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Affiliation(s)
- Abu Zahid Bin Aziz
- Department of Computer Science & Engineering, Rajshahi University of Engineering & Technology, Rajshahi, Bangladesh
- * E-mail:
| | - Md. Al Mehedi Hasan
- Department of Computer Science & Engineering, Rajshahi University of Engineering & Technology, Rajshahi, Bangladesh
| | - Jungpil Shin
- School of Computer Science and Engineering, University of Aizu, Aizuwakamatsu, Japan
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13
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Yang L, Gao H, Wu K, Zhang H, Li C, Tang L. Identification of Cancerlectins By Using Cascade Linear Discriminant Analysis and Optimal g-gap Tripeptide Composition. Curr Bioinform 2020. [DOI: 10.2174/1574893614666190730103156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background:
Lectins are a diverse group of glycoproteins or glycoconjugate proteins
that can be extracted from plants, invertebrates and higher animals. Cancerlectins, a kind of lectins,
which play a key role in the process of tumor cells interacting with each other and are being employed
as therapeutic agents. A full understanding of cancerlectins is significant because it provides
a tool for the future direction of cancer therapy.
Objective:
To develop an accurate and practically useful timesaving tool to identify cancerlectins.
A novel sequence-based method is proposed along with a correlative webserver to access the proposed
tool.
Methods:
Firstly, protein features were extracted in a newly feature building way termed, g-gap
tripeptide composition. After which a proposed cascade linear discriminant analysis (Cascade
LDA) is used to alleviate the high dimensional difficulties with the Analysis Of Variance (ANOVA)
as a feature importance criterion. Finally, Support Vector Machine (SVM) is used as the classifier
to identify cancerlectins.
Results:
The proposed method achieved an accuracy of 91.34% with sensitivity of 89.89%, specificity
of 92.48% and an 0.8318 Mathew’s correlation coefficient based on only 13 fusion features
in jackknife cross validation, the result of which is superior to other published methods in this domain.
Conclusion:
In this study, a new method based only on primary structure of protein is proposed
and experimental results show that it could be a promising tool to identify cancerlectins. An openaccess
webserver is made available in this work to facilitate other related works.
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Affiliation(s)
- Liangwei Yang
- Center for Informational Biology, School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Hui Gao
- Center for Informational Biology, School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Keyu Wu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Haotian Zhang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Changyu Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lixia Tang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
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14
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Liu GH, Zhang BW, Qian G, Wang B, Mao B, Bichindaritz I. Bioimage-Based Prediction of Protein Subcellular Location in Human Tissue with Ensemble Features and Deep Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1966-1980. [PMID: 31107658 DOI: 10.1109/tcbb.2019.2917429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Prediction of protein subcellular location has currently become a hot topic because it has been proven to be useful for understanding both the disease mechanisms and novel drug design. With the rapid development of automated microscopic imaging technology in recent years, classification methods of bioimage-based protein subcellular location have attracted considerable attention for images can describe the protein distribution intuitively and in detail. In the current study, a prediction method of protein subcellular location was proposed based on multi-view image features that are extracted from three different views, including the four texture features of the original image, the global and local features of the protein extracted from the protein channel images after color segmentation, and the global features of DNA extracted from the DNA channel image. Finally, the extracted features were combined together to improve the performance of subcellular localization prediction. From the performance comparison of different combination features under the same classifier, the best ensemble features could be obtained. In this work, a classifier based on Stacked Auto-encoders and the random forest was also put forward. To improve the prediction results, the deep network was combined with the traditional statistical classification methods. Stringent cross-validation and independent validation tests on the benchmark dataset demonstrated the efficacy of the proposed method.
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15
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Wang Y, Kang J, Li N, Zhou Y, Tang Z, He B, Huang J. NeuroCS: A Tool to Predict Cleavage Sites of Neuropeptide Precursors. Protein Pept Lett 2020; 27:337-345. [PMID: 31721688 DOI: 10.2174/0929866526666191112150636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/16/2019] [Accepted: 09/24/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neuropeptides are a class of bioactive peptides produced from neuropeptide precursors through a series of extremely complex processes, mediating neuronal regulations in many aspects. Accurate identification of cleavage sites of neuropeptide precursors is of great significance for the development of neuroscience and brain science. OBJECTIVE With the explosive growth of neuropeptide precursor data, it is pretty much needed to develop bioinformatics methods for predicting neuropeptide precursors' cleavage sites quickly and efficiently. METHODS We started with processing the neuropeptide precursor data from SwissProt and NueoPedia into two sets of data, training dataset and testing dataset. Subsequently, six feature extraction schemes were applied to generate different feature sets and then feature selection methods were used to find the optimal feature subset of each. Thereafter the support vector machine was utilized to build models for different feature types. Finally, the performance of models were evaluated with the independent testing dataset. RESULTS Six models are built through support vector machine. Among them the enhanced amino acid composition-based model reaches the highest accuracy of 91.60% in the 5-fold cross validation. When evaluated with independent testing dataset, it also showed an excellent performance with a high accuracy of 90.37% and Area under Receiver Operating Characteristic curve up to 0.9576. CONCLUSION The performance of the developed model was decent. Moreover, for users' convenience, an online web server called NeuroCS is built, which is freely available at http://i.uestc.edu.cn/NeuroCS/dist/index.html#/. NeuroCS can be used to predict neuropeptide precursors' cleavage sites effectively.
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Affiliation(s)
- Ying Wang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Juanjuan Kang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ning Li
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuwei Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhongjie Tang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Medical College, Guizhou University, Guiyang, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
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16
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Chen W, Nie F, Ding H. Recent Advances of Computational Methods for Identifying Bacteriophage Virion Proteins. Protein Pept Lett 2020; 27:259-264. [PMID: 30968770 DOI: 10.2174/0929866526666190410124642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/07/2019] [Accepted: 04/01/2019] [Indexed: 01/09/2023]
Abstract
Phage Virion Proteins (PVP) are essential materials of bacteriophage, which participate in a series of biological processes. Accurate identification of phage virion proteins is helpful to understand the mechanism of interaction between the phage and its host bacteria. Since experimental method is labor intensive and time-consuming, in the past few years, many computational approaches have been proposed to identify phage virion proteins. In order to facilitate researchers to select appropriate methods, it is necessary to give a comprehensive review and comparison on existing computational methods on identifying phage virion proteins. In this review, we summarized the existing computational methods for identifying phage virion proteins and also assessed their performances on an independent dataset. Finally, challenges and future perspectives for identifying phage virion proteins were presented. Taken together, we hope that this review could provide clues to researches on the study of phage virion proteins.
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Affiliation(s)
- Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China.,Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Fulei Nie
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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17
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Xu L, Liang G, Chen B, Tan X, Xiang H, Liao C. A Computational Method for the Identification of Endolysins and Autolysins. Protein Pept Lett 2020; 27:329-336. [PMID: 31577192 DOI: 10.2174/0929866526666191002104735] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/27/2019] [Accepted: 09/03/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cell lytic enzyme is a kind of highly evolved protein, which can destroy the cell structure and kill the bacteria. Compared with antibiotics, cell lytic enzyme will not cause serious problem of drug resistance of pathogenic bacteria. Thus, the study of cell wall lytic enzymes aims at finding an efficient way for curing bacteria infectious. Compared with using antibiotics, the problem of drug resistance becomes more serious. Therefore, it is a good choice for curing bacterial infections by using cell lytic enzymes. Cell lytic enzyme includes endolysin and autolysin and the difference between them is the purpose of the break of cell wall. The identification of the type of cell lytic enzymes is meaningful for the study of cell wall enzymes. OBJECTIVE In this article, our motivation is to predict the type of cell lytic enzyme. Cell lytic enzyme is helpful for killing bacteria, so it is meaningful for study the type of cell lytic enzyme. However, it is time consuming to detect the type of cell lytic enzyme by experimental methods. Thus, an efficient computational method for the type of cell lytic enzyme prediction is proposed in our work. METHODS We propose a computational method for the prediction of endolysin and autolysin. First, a data set containing 27 endolysins and 41 autolysins is built. Then the protein is represented by tripeptides composition. The features are selected with larger confidence degree. At last, the classifier is trained by the labeled vectors based on support vector machine. The learned classifier is used to predict the type of cell lytic enzyme. RESULTS Following the proposed method, the experimental results show that the overall accuracy can attain 97.06%, when 44 features are selected. Compared with Ding's method, our method improves the overall accuracy by nearly 4.5% ((97.06-92.9)/92.9%). The performance of our proposed method is stable, when the selected feature number is from 40 to 70. The overall accuracy of tripeptides optimal feature set is 94.12%, and the overall accuracy of Chou's amphiphilic PseAAC method is 76.2%. The experimental results also demonstrate that the overall accuracy is improved by nearly 18% when using the tripeptides optimal feature set. CONCLUSION The paper proposed an efficient method for identifying endolysin and autolysin. In this paper, support vector machine is used to predict the type of cell lytic enzyme. The experimental results show that the overall accuracy of the proposed method is 94.12%, which is better than some existing methods. In conclusion, the selected 44 features can improve the overall accuracy for identification of the type of cell lytic enzyme. Support vector machine performs better than other classifiers when using the selected feature set on the benchmark data set.
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Affiliation(s)
- Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Guangmin Liang
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Baowen Chen
- School of Software, Shenzhen Institute of Information Technology, Shenzhen, China
| | - Xu Tan
- School of Software, Shenzhen Institute of Information Technology, Shenzhen, China
| | - Huaikun Xiang
- School of Automotive and Transportation Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Changrui Liao
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
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18
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Khan F, Khan M, Iqbal N, Khan S, Muhammad Khan D, Khan A, Wei DQ. Prediction of Recombination Spots Using Novel Hybrid Feature Extraction Method via Deep Learning Approach. Front Genet 2020; 11:539227. [PMID: 33093842 PMCID: PMC7527634 DOI: 10.3389/fgene.2020.539227] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/13/2020] [Indexed: 01/20/2023] Open
Abstract
Meiotic recombination is the driving force of evolutionary development and an important source of genetic variation. The meiotic recombination does not take place randomly in a chromosome but occurs in some regions of the chromosome. A region in chromosomes with higher rate of meiotic recombination events are considered as hotspots and a region where frequencies of the recombination events are lower are called coldspots. Prediction of meiotic recombination spots provides useful information about the basic functionality of inheritance and genome diversity. This study proposes an intelligent computational predictor called iRSpots-DNN for the identification of recombination spots. The proposed predictor is based on a novel feature extraction method and an optimized deep neural network (DNN). The DNN was employed as a classification engine whereas, the novel features extraction method was developed to extract meaningful features for the identification of hotspots and coldspots across the yeast genome. Unlike previous algorithms, the proposed feature extraction avoids bias among different selected features and preserved the sequence discriminant properties along with the sequence-structure information simultaneously. This study also considered other effective classifiers named support vector machine (SVM), K-nearest neighbor (KNN), and random forest (RF) to predict recombination spots. Experimental results on a benchmark dataset with 10-fold cross-validation showed that iRSpots-DNN achieved the highest accuracy, i.e., 95.81%. Additionally, the performance of the proposed iRSpots-DNN is significantly better than the existing predictors on a benchmark dataset. The relevant benchmark dataset and source code are freely available at: https://github.com/Fatima-Khan12/iRspot_DNN/tree/master/iRspot_DNN.
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Affiliation(s)
- Fatima Khan
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mukhtaj Khan
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Nadeem Iqbal
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Salman Khan
- Department of Computer Science, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Dost Muhammad Khan
- Department of Statistics, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Ministry of Education, Shanghai, China.,Peng Cheng Laboratory, Shenzhen, China
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19
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Xu ZC, Feng PM, Yang H, Qiu WR, Chen W, Lin H. iRNAD: a computational tool for identifying D modification sites in RNA sequence. Bioinformatics 2020; 35:4922-4929. [PMID: 31077296 DOI: 10.1093/bioinformatics/btz358] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/01/2019] [Accepted: 04/27/2019] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased in cancerous tissues. Therefore, it is necessary to detect D in RNA for further understanding its functional roles. Since wet-experimental techniques for the aim are time-consuming and laborious, it is urgent to develop computational models to identify D modification sites in RNA. RESULTS We constructed a predictor, called iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the classification. The final model could produce the overall accuracy of 96.18% with the area under the receiver operating characteristic curve of 0.9839 in jackknife cross-validation test. Furthermore, we performed a series of validations from several aspects and demonstrated the robustness and reliability of the proposed model. AVAILABILITY AND IMPLEMENTATION A user-friendly web-server called iRNAD can be freely accessible at http://lin-group.cn/server/iRNAD, which will provide convenience and guide to users for further studying D modification.
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Affiliation(s)
- Zhao-Chun Xu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.,Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Peng-Mian Feng
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wang-Ren Qiu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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20
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Saikia S, Bordoloi M, Sarmah R. Established and In-trial GPCR Families in Clinical Trials: A Review for Target Selection. Curr Drug Targets 2020; 20:522-539. [PMID: 30394207 DOI: 10.2174/1389450120666181105152439] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/28/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022]
Abstract
The largest family of drug targets in clinical trials constitute of GPCRs (G-protein coupled receptors) which accounts for about 34% of FDA (Food and Drug Administration) approved drugs acting on 108 unique GPCRs. Factors such as readily identifiable conserved motif in structures, 127 orphan GPCRs despite various de-orphaning techniques, directed functional antibodies for validation as drug targets, etc. has widened their therapeutic windows. The availability of 44 crystal structures of unique receptors, unexplored non-olfactory GPCRs (encoded by 50% of the human genome) and 205 ligand receptor complexes now present a strong foundation for structure-based drug discovery and design. The growing impact of polypharmacology for complex diseases like schizophrenia, cancer etc. warrants the need for novel targets and considering the undiscriminating and selectivity of GPCRs, they can fulfill this purpose. Again, natural genetic variations within the human genome sometimes delude the therapeutic expectations of some drugs, resulting in medication response differences and ADRs (adverse drug reactions). Around ~30 billion US dollars are dumped annually for poor accounting of ADRs in the US alone. To curb such undesirable reactions, the knowledge of established and currently in clinical trials GPCRs families can offer huge understanding towards the drug designing prospects including "off-target" effects reducing economical resource and time. The druggability of GPCR protein families and critical roles played by them in complex diseases are explained. Class A, class B1, class C and class F are generally established family and GPCRs in phase I (19%), phase II(29%), phase III(52%) studies are also reviewed. From the phase I studies, frizzled receptors accounted for the highest in trial targets, neuropeptides in phase II and melanocortin in phase III studies. Also, the bioapplications for nanoparticles along with future prospects for both nanomedicine and GPCR drug industry are discussed. Further, the use of computational techniques and methods employed for different target validations are also reviewed along with their future potential for the GPCR based drug discovery.
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Affiliation(s)
- Surovi Saikia
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Manobjyoti Bordoloi
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Rajeev Sarmah
- Allied Health Sciences, Assam Down Town University, Panikhaiti, Guwahati 781026, Assam, India
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21
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Gong J, Chen Y, Pu F, Sun P, He F, Zhang L, Li Y, Ma Z, Wang H. Understanding Membrane Protein Drug Targets in Computational Perspective. Curr Drug Targets 2020; 20:551-564. [PMID: 30516106 DOI: 10.2174/1389450120666181204164721] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 01/16/2023]
Abstract
Membrane proteins play crucial physiological roles in vivo and are the major category of drug targets for pharmaceuticals. The research on membrane protein is a significant part in the drug discovery. The biological process is a cycled network, and the membrane protein is a vital hub in the network since most drugs achieve the therapeutic effect via interacting with the membrane protein. In this review, typical membrane protein targets are described, including GPCRs, transporters and ion channels. Also, we conclude network servers and databases that are referring to the drug, drug-target information and their relevant data. Furthermore, we chiefly introduce the development and practice of modern medicines, particularly demonstrating a series of state-of-the-art computational models for the prediction of drug-target interaction containing network-based approach and machine-learningbased approach as well as showing current achievements. Finally, we discuss the prospective orientation of drug repurposing and drug discovery as well as propose some improved framework in bioactivity data, created or improved predicted approaches, alternative understanding approaches of drugs bioactivity and their biological processes.
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Affiliation(s)
- Jianting Gong
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Yongbing Chen
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Feng Pu
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Pingping Sun
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Fei He
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Li Zhang
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, China
| | - Yanwen Li
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Zhiqiang Ma
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Han Wang
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
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22
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Feng P, Wang Z. Recent Advances in Computational Methods for Identifying Anticancer Peptides. Curr Drug Targets 2020; 20:481-487. [PMID: 30068270 DOI: 10.2174/1389450119666180801121548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/28/2018] [Accepted: 05/28/2018] [Indexed: 01/10/2023]
Abstract
Anticancer peptide (ACP) is a kind of small peptides that can kill cancer cells without damaging normal cells. In recent years, ACP has been pre-clinically used for cancer treatment. Therefore, accurate identification of ACPs will promote their clinical applications. In contrast to labor-intensive experimental techniques, a series of computational methods have been proposed for identifying ACPs. In this review, we briefly summarized the current progress in computational identification of ACPs. The challenges and future perspectives in developing reliable methods for identification of ACPs were also discussed. We anticipate that this review could provide novel insights into future researches on anticancer peptides.
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Affiliation(s)
- Pengmian Feng
- School of Public Health, North China University of Science and Technology, Tangshan, 063000, China
| | - Zhenyi Wang
- Center for Genomics and Computational Biology, School of Life Science, North China University of Science and Technology, Tangshan, 063000, China
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23
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Wang L, Zhang R. Towards Computational Models of Identifying Protein Ubiquitination Sites. Curr Drug Targets 2020; 20:565-578. [PMID: 30246637 DOI: 10.2174/1389450119666180924150202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/29/2018] [Accepted: 09/04/2018] [Indexed: 12/25/2022]
Abstract
Ubiquitination is an important post-translational modification (PTM) process for the regulation of protein functions, which is associated with cancer, cardiovascular and other diseases. Recent initiatives have focused on the detection of potential ubiquitination sites with the aid of physicochemical test approaches in conjunction with the application of computational methods. The identification of ubiquitination sites using laboratory tests is especially susceptible to the temporality and reversibility of the ubiquitination processes, and is also costly and time-consuming. It has been demonstrated that computational methods are effective in extracting potential rules or inferences from biological sequence collections. Up to the present, the computational strategy has been one of the critical research approaches that have been applied for the identification of ubiquitination sites, and currently, there are numerous state-of-the-art computational methods that have been developed from machine learning and statistical analysis to undertake such work. In the present study, the construction of benchmark datasets is summarized, together with feature representation methods, feature selection approaches and the classifiers involved in several previous publications. In an attempt to explore pertinent development trends for the identification of ubiquitination sites, an independent test dataset was constructed and the predicting results obtained from five prediction tools are reported here, together with some related discussions.
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Affiliation(s)
- Lidong Wang
- College of Science, Dalian Maritime University, Dalian, China
| | - Ruijun Zhang
- College of Science, Dalian Maritime University, Dalian, China
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24
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Tan JX, Lv H, Wang F, Dao FY, Chen W, Ding H. A Survey for Predicting Enzyme Family Classes Using Machine Learning Methods. Curr Drug Targets 2020; 20:540-550. [PMID: 30277150 DOI: 10.2174/1389450119666181002143355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/17/2018] [Accepted: 09/04/2018] [Indexed: 12/13/2022]
Abstract
Enzymes are proteins that act as biological catalysts to speed up cellular biochemical processes. According to their main Enzyme Commission (EC) numbers, enzymes are divided into six categories: EC-1: oxidoreductase; EC-2: transferase; EC-3: hydrolase; EC-4: lyase; EC-5: isomerase and EC-6: synthetase. Different enzymes have different biological functions and acting objects. Therefore, knowing which family an enzyme belongs to can help infer its catalytic mechanism and provide information about the relevant biological function. With the large amount of protein sequences influxing into databanks in the post-genomics age, the annotation of the family for an enzyme is very important. Since the experimental methods are cost ineffective, bioinformatics tool will be a great help for accurately classifying the family of the enzymes. In this review, we summarized the application of machine learning methods in the prediction of enzyme family from different aspects. We hope that this review will provide insights and inspirations for the researches on enzyme family classification.
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Affiliation(s)
- Jiu-Xin Tan
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Fang Wang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.,Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China.,Gordon Life Science Institute, Boston, MA 02478, United States
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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25
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Abstract
Background:Pseudouridine (Ψ) is the most abundant RNA modification and has important functions in a series of biological and cellular processes. Although experimental techniques have made great contributions to identify Ψ sites, they are still labor-intensive and costineffective. In the past few years, a series of computational approaches have been developed, which provided rapid and efficient approaches to identify Ψ sites.Results:To provide the readership with a clear landscape about the recent development in this important area, in this review, we summarized and compared the representative computational approaches developed for identifying Ψ sites. Moreover, future directions in computationally identifying Ψ sites were discussed as well.Conclusion:We anticipate that this review will provide novel insights into the researches on pseudouridine modification.
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Affiliation(s)
- Wei Chen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063210, China
| | - Kewei Liu
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063210, China
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26
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27
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Feng CQ, Zhang ZY, Zhu XJ, Lin Y, Chen W, Tang H, Lin H. iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators. Bioinformatics 2020; 35:1469-1477. [PMID: 30247625 DOI: 10.1093/bioinformatics/bty827] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Transcription termination is an important regulatory step of gene expression. If there is no terminator in gene, transcription could not stop, which will result in abnormal gene expression. Detecting such terminators can determine the operon structure in bacterial organisms and improve genome annotation. Thus, accurate identification of transcriptional terminators is essential and extremely important in the research of transcription regulations. RESULTS In this study, we developed a new predictor called 'iTerm-PseKNC' based on support vector machine to identify transcription terminators. The binomial distribution approach was used to pick out the optimal feature subset derived from pseudo k-tuple nucleotide composition (PseKNC). The 5-fold cross-validation test results showed that our proposed method achieved an accuracy of 95%. To further evaluate the generalization ability of 'iTerm-PseKNC', the model was examined on independent datasets which are experimentally confirmed Rho-independent terminators in Escherichia coli and Bacillus subtilis genomes. As a result, all the terminators in E. coli and 87.5% of the terminators in B. subtilis were correctly identified, suggesting that the proposed model could become a powerful tool for bacterial terminator recognition. AVAILABILITY AND IMPLEMENTATION For the convenience of most of wet-experimental researchers, the web-server for 'iTerm-PseKNC' was established at http://lin-group.cn/server/iTerm-PseKNC/, by which users can easily obtain their desired result without the need to go through the detailed mathematical equations involved.
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Affiliation(s)
- Chao-Qin Feng
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhao-Yue Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiao-Juan Zhu
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Lin
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Hua Tang
- Department of Pathophysiology, Southwest Medical University, Luzhou, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC. PLoS One 2020; 15:e0228479. [PMID: 32413030 PMCID: PMC7228126 DOI: 10.1371/journal.pone.0228479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/01/2020] [Indexed: 11/19/2022] Open
Abstract
Terminator is a DNA sequence that gives the RNA polymerase the transcriptional termination signal. Identifying terminators correctly can optimize the genome annotation, more importantly, it has considerable application value in disease diagnosis and therapies. However, accurate prediction methods are deficient and in urgent need. Therefore, we proposed a prediction method "iterb-PPse" for terminators by incorporating 47 nucleotide properties into PseKNC-Ⅰ and PseKNC-Ⅱ and utilizing Extreme Gradient Boosting to predict terminators based on Escherichia coli and Bacillus subtilis. Combing with the preceding methods, we employed three new feature extraction methods K-pwm, Base-content, Nucleotidepro to formulate raw samples. The two-step method was applied to select features. When identifying terminators based on optimized features, we compared five single models as well as 16 ensemble models. As a result, the accuracy of our method on benchmark dataset achieved 99.88%, higher than the existing state-of-the-art predictor iTerm-PseKNC in 100 times five-fold cross-validation test. Its prediction accuracy for two independent datasets reached 94.24% and 99.45% respectively. For the convenience of users, we developed a software on the basis of "iterb-PPse" with the same name. The open software and source code of "iterb-PPse" are available at https://github.com/Sarahyouzi/iterb-PPse.
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Li J, Huang Y, Zhou Y. A Mini-review of the Computational Methods Used in Identifying RNA 5-Methylcytosine Sites. Curr Genomics 2020; 21:3-10. [PMID: 32655293 PMCID: PMC7324889 DOI: 10.2174/2213346107666200219124951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/17/2020] [Accepted: 01/31/2020] [Indexed: 01/10/2023] Open
Abstract
RNA 5-methylcytosine (m5C) is one of the pillars of post-transcriptional modification (PTCM). A growing body of evidence suggests that m5C plays a vital role in RNA metabolism. Accurate localization of RNA m5C sites in tissue cells is the premise and basis for the in-depth understanding of the functions of m5C. However, the main experimental methods of detecting m5C sites are limited to varying degrees. Establishing a computational model to predict modification sites is an excellent complement to wet experiments for identifying m5C sites. In this review, we summarized some available m5C predictors and discussed the characteristics of these methods.
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Affiliation(s)
- Jianwei Li
- 1Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, China; 2Department of Biomedical Informatics, School of Basic Medical Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing, China
| | - Yan Huang
- 1Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, China; 2Department of Biomedical Informatics, School of Basic Medical Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing, China
| | - Yuan Zhou
- 1Institute of Computational Medicine, School of Artificial Intelligence, Hebei University of Technology, Tianjin, China; 2Department of Biomedical Informatics, School of Basic Medical Sciences, Center for Noncoding RNA Medicine, Peking University, Beijing, China
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iPseU-Layer: Identifying RNA Pseudouridine Sites Using Layered Ensemble Model. Interdiscip Sci 2020; 12:193-203. [PMID: 32170573 DOI: 10.1007/s12539-020-00362-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 01/28/2023]
Abstract
Pseudouridine represents one of the most prevalent post-transcriptional RNA modifications. The identification of pseudouridine sites is an essential step toward understanding RNA functions, RNA structure stabilization, translation process, and RNA stability; however, high-throughput experimental techniques remain expensive and time-consuming in lab explorations and biochemical processes. Thus, how to develop an efficient pseudouridine site identification method based on machine learning is very important both in academic research and drug development. Motived by this, we present an effective layered ensemble model designated as iPseU-Layer for identification of RNA pseudouridine sites. The proposed iPseU-Layer approach is essentially based on three different machine learning layers including: feature selection layer, feature extraction and fusion layer, and prediction layer. The feature selection layer reduces the dimensionality, which can be regarded as a data pre-processing stage. The feature extraction and fusion layer utilizes an ensemble method which is implemented through various machine learning algorithms to generate some outputs. The prediction layer applies classic random forest to identify the final results. Furthermore, we systematically conduct the validation experiments using cross-validation tests and independent test with the current state-of-the-art models. The proposed iPseU-Layer provides a promising predictive performance in terms of sensitivity, specificity, accuracy and Matthews correlation coefficient. Collectively, these findings indicate that the framework of iPseU-Layer is a feasible and effective strategy for the prediction of RNA pseudouridine sites.
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Liu T, Tang H. A Brief Survey of Machine Learning Methods in Identification of Mitochondria Proteins in Malaria Parasite. Curr Pharm Des 2020; 26:3049-3058. [PMID: 32156226 DOI: 10.2174/1381612826666200310122324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 02/10/2020] [Indexed: 11/22/2022]
Abstract
The number of human deaths caused by malaria is increasing day-by-day. In fact, the mitochondrial proteins of the malaria parasite play vital roles in the organism. For developing effective drugs and vaccines against infection, it is necessary to accurately identify mitochondrial proteins of the malaria parasite. Although precise details for the mitochondrial proteins can be provided by biochemical experiments, they are expensive and time-consuming. In this review, we summarized the machine learning-based methods for mitochondrial proteins identification in the malaria parasite and compared the construction strategies of these computational methods. Finally, we also discussed the future development of mitochondrial proteins recognition with algorithms.
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Affiliation(s)
- Ting Liu
- Department of Pathophysiology, Key Laboratory of Medical Electrophysiology, Ministry of Education, Southwest Medical University, Luzhou 646000, China
| | - Hua Tang
- Department of Pathophysiology, Key Laboratory of Medical Electrophysiology, Ministry of Education, Southwest Medical University, Luzhou 646000, China
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32
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Wei L, Luan S, Nagai LAE, Su R, Zou Q. Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species. Bioinformatics 2020; 35:1326-1333. [PMID: 30239627 DOI: 10.1093/bioinformatics/bty824] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) is recently shown to play crucial roles in restriction-modification systems. For better understanding of their functional mechanisms, it is fundamentally important to identify 4mC modification. Machine learning methods have recently emerged as an effective and efficient approach for the high-throughput identification of 4mC sites, although high predictive error rates are still challenging for existing methods. Therefore, it is highly desirable to develop a computational method to more accurately identify m4C sites. RESULTS In this study, we propose a machine learning based predictor, namely 4mcPred-SVM, for the genome-wide detection of DNA 4mC sites. In this predictor, we present a new feature representation algorithm that sufficiently exploits sequence-based information. To improve the feature representation ability, we use a two-step feature optimization strategy, thereby obtaining the most representative features. Using the resulting features and Support Vector Machine (SVM), we adaptively train the optimal models for different species. Comparative results on benchmark datasets from six species indicate that our predictor is able to achieve generally better performance in predicting 4mC sites as compared to the state-of-the-art predictors. Importantly, the sequence-based features can reliably and robust predict 4mC sites, facilitating the discovery of potentially important sequence characteristics for the prediction of 4mC sites. AVAILABILITY AND IMPLEMENTATION The user-friendly webserver that implements the proposed 4mcPred-SVM is well established, and is freely accessible at http://server.malab.cn/4mcPred-SVM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Leyi Wei
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Shasha Luan
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Luis Augusto Eijy Nagai
- Lab of Functional Analysis In Silico, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ran Su
- School of Computer Software, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Quan Zou
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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Some illuminating remarks on molecular genetics and genomics as well as drug development. Mol Genet Genomics 2020; 295:261-274. [PMID: 31894399 DOI: 10.1007/s00438-019-01634-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
Facing the explosive growth of biological sequences unearthed in the post-genomic age, one of the most important but also most difficult problems in computational biology is how to express a biological sequence with a discrete model or a vector, but still keep it with considerable sequence-order information or its special pattern. To deal with such a challenging problem, the ideas of "pseudo amino acid components" and "pseudo K-tuple nucleotide composition" have been proposed. The ideas and their approaches have further stimulated the birth for "distorted key theory", "wenxing diagram", and substantially strengthening the power in treating the multi-label systems, as well as the establishment of the famous "5-steps rule". All these logic developments are quite natural that are very useful not only for theoretical scientists but also for experimental scientists in conducting genetics/genomics analysis and drug development. Presented in this review paper are also their future perspectives; i.e., their impacts will become even more significant and propounding.
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Shao YT, Liu XX, Lu Z, Chou KC. pLoc_Deep-mHum: Predict Subcellular Localization of Human Proteins by Deep Learning. ACTA ACUST UNITED AC 2020. [DOI: 10.4236/ns.2020.127042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Shao Y, Chou KC. pLoc_Deep-mEuk: Predict Subcellular Localization of Eukaryotic Proteins by Deep Learning. ACTA ACUST UNITED AC 2020. [DOI: 10.4236/ns.2020.126034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Basith S, Manavalan B, Shin TH, Lee G. SDM6A: A Web-Based Integrative Machine-Learning Framework for Predicting 6mA Sites in the Rice Genome. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:131-141. [PMID: 31542696 PMCID: PMC6796762 DOI: 10.1016/j.omtn.2019.08.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/30/2019] [Accepted: 08/08/2019] [Indexed: 12/19/2022]
Abstract
DNA N6-adenine methylation (6mA) is an epigenetic modification in prokaryotes and eukaryotes. Identifying 6mA sites in rice genome is important in rice epigenetics and breeding, but non-random distribution and biological functions of these sites remain unclear. Several machine-learning tools can identify 6mA sites but show limited prediction accuracy, which limits their usability in epigenetic research. Here, we developed a novel computational predictor, called the Sequence-based DNA N6-methyladenine predictor (SDM6A), which is a two-layer ensemble approach for identifying 6mA sites in the rice genome. Unlike existing methods, which are based on single models with basic features, SDM6A explores various features, and five encoding methods were identified as appropriate for this problem. Subsequently, an optimal feature set was identified from encodings, and corresponding models were developed individually using support vector machine and extremely randomized tree. First, all five single models were integrated via ensemble approach to define the class for each classifier. Second, two classifiers were integrated to generate a final prediction. SDM6A achieved robust performance on cross-validation and independent evaluation, with average accuracy and Matthews correlation coefficient (MCC) of 88.2% and 0.764, respectively. Corresponding metrics were 4.7%-11.0% and 2.3%-5.5% higher than those of existing methods, respectively. A user-friendly, publicly accessible web server (http://thegleelab.org/SDM6A) was implemented to predict novel putative 6mA sites in rice genome.
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Affiliation(s)
- Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | | | - Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea.
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37
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Javed F, Hayat M. Predicting subcellular localization of multi-label proteins by incorporating the sequence features into Chou's PseAAC. Genomics 2019; 111:1325-1332. [DOI: 10.1016/j.ygeno.2018.09.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 09/04/2018] [Indexed: 12/13/2022]
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38
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pLoc_bal-mHum: Predict subcellular localization of human proteins by PseAAC and quasi-balancing training dataset. Genomics 2019; 111:1274-1282. [DOI: 10.1016/j.ygeno.2018.08.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 12/17/2022]
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39
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iRSpot-DTS: Predict recombination spots by incorporating the dinucleotide-based spare-cross covariance information into Chou's pseudo components. Genomics 2019; 111:1760-1770. [DOI: 10.1016/j.ygeno.2018.11.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022]
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40
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Chou KC. Impacts of Pseudo Amino Acid Components and 5-steps Rule to Proteomics and Proteome Analysis. Curr Top Med Chem 2019; 19:2283-2300. [DOI: 10.2174/1568026619666191018100141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/18/2019] [Accepted: 08/26/2019] [Indexed: 01/27/2023]
Abstract
Stimulated by the 5-steps rule during the last decade or so, computational proteomics has achieved remarkable progresses in the following three areas: (1) protein structural class prediction; (2) protein subcellular location prediction; (3) post-translational modification (PTM) site prediction. The results obtained by these predictions are very useful not only for an in-depth study of the functions of proteins and their biological processes in a cell, but also for developing novel drugs against major diseases such as cancers, Alzheimer’s, and Parkinson’s. Moreover, since the targets to be predicted may have the multi-label feature, two sets of metrics are introduced: one is for inspecting the global prediction quality, while the other for the local prediction quality. All the predictors covered in this review have a userfriendly web-server, through which the majority of experimental scientists can easily obtain their desired data without the need to go through the complicated mathematics.
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Affiliation(s)
- Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
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41
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Li F, Wang Y, Li C, Marquez-Lago TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Ian Smith A, Lithgow T, Daly RJ, Whisstock JC, Song J. Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. Brief Bioinform 2019; 20:2150-2166. [PMID: 30184176 PMCID: PMC6954447 DOI: 10.1093/bib/bby077] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 01/06/2023] Open
Abstract
The roles of proteolytic cleavage have been intensively investigated and discussed during the past two decades. This irreversible chemical process has been frequently reported to influence a number of crucial biological processes (BPs), such as cell cycle, protein regulation and inflammation. A number of advanced studies have been published aiming at deciphering the mechanisms of proteolytic cleavage. Given its significance and the large number of functionally enriched substrates targeted by specific proteases, many computational approaches have been established for accurate prediction of protease-specific substrates and their cleavage sites. Consequently, there is an urgent need to systematically assess the state-of-the-art computational approaches for protease-specific cleavage site prediction to further advance the existing methodologies and to improve the prediction performance. With this goal in mind, in this article, we carefully evaluated a total of 19 computational methods (including 8 scoring function-based methods and 11 machine learning-based methods) in terms of their underlying algorithm, calculated features, performance evaluation and software usability. Then, extensive independent tests were performed to assess the robustness and scalability of the reviewed methods using our carefully prepared independent test data sets with 3641 cleavage sites (specific to 10 proteases). The comparative experimental results demonstrate that PROSPERous is the most accurate generic method for predicting eight protease-specific cleavage sites, while GPS-CCD and LabCaS outperformed other predictors for calpain-specific cleavage sites. Based on our review, we then outlined some potential ways to improve the prediction performance and ease the computational burden by applying ensemble learning, deep learning, positive unlabeled learning and parallel and distributed computing techniques. We anticipate that our study will serve as a practical and useful guide for interested readers to further advance next-generation bioinformatics tools for protease-specific cleavage site prediction.
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Affiliation(s)
- Fuyi Li
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Yanan Wang
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Department of Biology, Institute of Molecular Systems Biology,ETH Zürich, Zürich 8093, Switzerland
| | - Tatiana T Marquez-Lago
- Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - André Leier
- Department of Genetics and Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - Neil D Rawlings
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Wellcome Trust Genome Campus,Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gholamreza Haffari
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Jerico Revote
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA 02478, USA
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Robert N Pike
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - A Ian Smith
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Trevor Lithgow
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia
| | - Roger J Daly
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - James C Whisstock
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
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Xie NZ, Li JX, Huang RB. Biological Production of (S)-acetoin: A State-of-the-Art Review. Curr Top Med Chem 2019; 19:2348-2356. [PMID: 31648637 DOI: 10.2174/1568026619666191018111424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 12/24/2022]
Abstract
Acetoin is an important four-carbon compound that has many applications in foods, chemical synthesis, cosmetics, cigarettes, soaps, and detergents. Its stereoisomer (S)-acetoin, a high-value chiral compound, can also be used to synthesize optically active drugs, which could enhance targeting properties and reduce side effects. Recently, considerable progress has been made in the development of biotechnological routes for (S)-acetoin production. In this review, various strategies for biological (S)- acetoin production are summarized, and their constraints and possible solutions are described. Furthermore, future prospects of biological production of (S)-acetoin are discussed.
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Affiliation(s)
- Neng-Zhong Xie
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Jian-Xiu Li
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Ri-Bo Huang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China
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43
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Chou KC. Advances in Predicting Subcellular Localization of Multi-label Proteins and its Implication for Developing Multi-target Drugs. Curr Med Chem 2019; 26:4918-4943. [PMID: 31060481 DOI: 10.2174/0929867326666190507082559] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/16/2022]
Abstract
The smallest unit of life is a cell, which contains numerous protein molecules. Most
of the functions critical to the cell’s survival are performed by these proteins located in its different
organelles, usually called ‘‘subcellular locations”. Information of subcellular localization
for a protein can provide useful clues about its function. To reveal the intricate pathways at the
cellular level, knowledge of the subcellular localization of proteins in a cell is prerequisite.
Therefore, one of the fundamental goals in molecular cell biology and proteomics is to determine
the subcellular locations of proteins in an entire cell. It is also indispensable for prioritizing
and selecting the right targets for drug development. Unfortunately, it is both timeconsuming
and costly to determine the subcellular locations of proteins purely based on experiments.
With the avalanche of protein sequences generated in the post-genomic age, it is highly
desired to develop computational methods for rapidly and effectively identifying the subcellular
locations of uncharacterized proteins based on their sequences information alone. Actually,
considerable progresses have been achieved in this regard. This review is focused on those
methods, which have the capacity to deal with multi-label proteins that may simultaneously
exist in two or more subcellular location sites. Protein molecules with this kind of characteristic
are vitally important for finding multi-target drugs, a current hot trend in drug development.
Focused in this review are also those methods that have use-friendly web-servers established so
that the majority of experimental scientists can use them to get the desired results without the
need to go through the detailed mathematics involved.
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Affiliation(s)
- Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA 02478, United States
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44
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Kang C. 19F-NMR in Target-based Drug Discovery. Curr Med Chem 2019; 26:4964-4983. [PMID: 31187703 DOI: 10.2174/0929867326666190610160534] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/14/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.
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Affiliation(s)
- CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
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45
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Su ZD, Huang Y, Zhang ZY, Zhao YW, Wang D, Chen W, Chou KC, Lin H. iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC. Bioinformatics 2019; 34:4196-4204. [PMID: 29931187 DOI: 10.1093/bioinformatics/bty508] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Motivation Long non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. They have important functions in cell development and metabolism, such as genetic markers, genome rearrangements, chromatin modifications, cell cycle regulation, transcription and translation. Their functions are generally closely related to their localization in the cell. Therefore, knowledge about their subcellular locations can provide very useful clues or preliminary insight into their biological functions. Although biochemical experiments could determine the localization of lncRNAs in a cell, they are both time-consuming and expensive. Therefore, it is highly desirable to develop bioinformatics tools for fast and effective identification of their subcellular locations. Results We developed a sequence-based bioinformatics tool called 'iLoc-lncRNA' to predict the subcellular locations of LncRNAs by incorporating the 8-tuple nucleotide features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. Rigorous jackknife tests have shown that the overall accuracy achieved by the new predictor on a stringent benchmark dataset is 86.72%, which is over 20% higher than that by the existing state-of-the-art predictor evaluated on the same tests. Availability and implementation A user-friendly webserver has been established at http://lin-group.cn/server/iLoc-LncRNA, by which users can easily obtain their desired results. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhen-Dong Su
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Huang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhao-Yue Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ya-Wei Zhao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dong Wang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.,Gordon Life Science Institute, Boston, MA, USA
| | - Kuo-Chen Chou
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Gordon Life Science Institute, Boston, MA, USA
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Gordon Life Science Institute, Boston, MA, USA
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46
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Abstract
The smallest unit of life is a cell, which contains numerous protein molecules. Most
of the functions critical to the cell’s survival are performed by these proteins located in its different
organelles, usually called ‘‘subcellular locations”. Information of subcellular localization
for a protein can provide useful clues about its function. To reveal the intricate pathways at the
cellular level, knowledge of the subcellular localization of proteins in a cell is prerequisite.
Therefore, one of the fundamental goals in molecular cell biology and proteomics is to determine
the subcellular locations of proteins in an entire cell. It is also indispensable for prioritizing
and selecting the right targets for drug development. Unfortunately, it is both timeconsuming
and costly to determine the subcellular locations of proteins purely based on experiments.
With the avalanche of protein sequences generated in the post-genomic age, it is highly
desired to develop computational methods for rapidly and effectively identifying the subcellular
locations of uncharacterized proteins based on their sequences information alone. Actually,
considerable progresses have been achieved in this regard. This review is focused on those
methods, which have the capacity to deal with multi-label proteins that may simultaneously
exist in two or more subcellular location sites. Protein molecules with this kind of characteristic
are vitally important for finding multi-target drugs, a current hot trend in drug development.
Focused in this review are also those methods that have use-friendly web-servers established so
that the majority of experimental scientists can use them to get the desired results without the
need to go through the detailed mathematics involved.
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Affiliation(s)
- Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA 02478, United States
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47
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Yang H, Yang W, Dao FY, Lv H, Ding H, Chen W, Lin H. A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae. Brief Bioinform 2019; 21:1568-1580. [PMID: 31633777 DOI: 10.1093/bib/bbz123] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 05/03/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is one of the most important driving forces of biological evolution, which is initiated by double-strand DNA breaks. Recombination has important roles in genome diversity and evolution. This review firstly provides a comprehensive survey of the 15 computational methods developed for identifying recombination hotspots in Saccharomyces cerevisiae. These computational methods were discussed and compared in terms of underlying algorithms, extracted features, predictive capability and practical utility. Subsequently, a more objective benchmark data set was constructed to develop a new predictor iRSpot-Pse6NC2.0 (http://lin-group.cn/server/iRSpot-Pse6NC2.0). To further demonstrate the generalization ability of these methods, we compared iRSpot-Pse6NC2.0 with existing methods on the chromosome XVI of S. cerevisiae. The results of the independent data set test demonstrated that the new predictor is superior to existing tools in the identification of recombination hotspots. The iRSpot-Pse6NC2.0 will become an important tool for identifying recombination hotspot.
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Affiliation(s)
- Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wuritu Yang
- Development and Planning Department, Inner Mongolia University, Hohhot 010021, China
| | - Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Hao Lin
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, China
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48
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Liu B, Li K, Huang DS, Chou KC. iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach. Bioinformatics 2019; 34:3835-3842. [PMID: 29878118 DOI: 10.1093/bioinformatics/bty458] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/06/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Identification of enhancers and their strength is important because they play a critical role in controlling gene expression. Although some bioinformatics tools were developed, they are limited in discriminating enhancers from non-enhancers only. Recently, a two-layer predictor called 'iEnhancer-2L' was developed that can be used to predict the enhancer's strength as well. However, its prediction quality needs further improvement to enhance the practical application value. Results A new predictor called 'iEnhancer-EL' was proposed that contains two layer predictors: the first one (for identifying enhancers) is formed by fusing an array of six key individual classifiers, and the second one (for their strength) formed by fusing an array of ten key individual classifiers. All these key classifiers were selected from 171 elementary classifiers formed by SVM (Support Vector Machine) based on kmer, subsequence profile and PseKNC (Pseudo K-tuple Nucleotide Composition), respectively. Rigorous cross-validations have indicated that the proposed predictor is remarkably superior to the existing state-of-the-art one in this area. Availability and implementation A web server for the iEnhancer-EL has been established at http://bioinformatics.hitsz.edu.cn/iEnhancer-EL/, by which users can easily get their desired results without the need to go through the mathematical details. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China.,Gordon Life Science Institute, Belmont, MA, USA
| | - Kai Li
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Belmont, MA, USA.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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49
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Identifying DNase I hypersensitive sites using multi-features fusion and F-score features selection via Chou's 5-steps rule. Biophys Chem 2019; 253:106227. [DOI: 10.1016/j.bpc.2019.106227] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 01/12/2023]
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50
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Lv H, Dao FY, Guan ZX, Zhang D, Tan JX, Zhang Y, Chen W, Lin H. iDNA6mA-Rice: A Computational Tool for Detecting N6-Methyladenine Sites in Rice. Front Genet 2019; 10:793. [PMID: 31552096 PMCID: PMC6746913 DOI: 10.3389/fgene.2019.00793] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
DNA N6-methyladenine (6mA) is a dominant DNA modification form and involved in many biological functions. The accurate genome-wide identification of 6mA sites may increase understanding of its biological functions. Experimental methods for 6mA detection in eukaryotes genome are laborious and expensive. Therefore, it is necessary to develop computational methods to identify 6mA sites on a genomic scale, especially for plant genomes. Based on this consideration, the study aims to develop a machine learning-based method of predicting 6mA sites in the rice genome. We initially used mono-nucleotide binary encoding to formulate positive and negative samples. Subsequently, the machine learning algorithm named Random Forest was utilized to perform the classification for identifying 6mA sites. Our proposed method could produce an area under the receiver operating characteristic curve of 0.964 with an overall accuracy of 0.917, as indicated by the fivefold cross-validation test. Furthermore, an independent dataset was established to assess the generalization ability of our method. Finally, an area under the receiver operating characteristic curve of 0.981 was obtained, suggesting that the proposed method had good performance of predicting 6mA sites in the rice genome. For the convenience of retrieving 6mA sites, on the basis of the computational method, we built a freely accessible web server named iDNA6mA-Rice at http://lin-group.cn/server/iDNA6mA-Rice.
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Affiliation(s)
- Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zheng-Xing Guan
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiu-Xin Tan
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yong Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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