2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function
Involved with important cellular or gene functions and implicated with many kinds of cancers, piRNAs, or piwi-interacting RNAs, are of small non-coding RNA with around 19–33 nt in length. Given a small non-coding RNA molecule, can we predict whether it is of piRNA according to its sequence informati...
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| Format: | Article |
| Language: | English |
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Elsevier
2017-06-01
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| Series: | Molecular Therapy: Nucleic Acids |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2162253117301580 |
| _version_ | 1818254078619156480 |
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| author | Bin Liu Fan Yang Kuo-Chen Chou |
| author_facet | Bin Liu Fan Yang Kuo-Chen Chou |
| author_sort | Bin Liu |
| collection | DOAJ |
| description | Involved with important cellular or gene functions and implicated with many kinds of cancers, piRNAs, or piwi-interacting RNAs, are of small non-coding RNA with around 19–33 nt in length. Given a small non-coding RNA molecule, can we predict whether it is of piRNA according to its sequence information alone? Furthermore, there are two types of piRNA: one has the function of instructing target mRNA deadenylation, and the other does not. Can we discriminate one from the other? With the avalanche of RNA sequences emerging in the postgenomic age, it is urgent to address the two problems for both basic research and drug development. Unfortunately, to the best of our knowledge, so far no computational methods whatsoever could be used to deal with the second problem, let alone deal with the two problems together. Here, by incorporating the physicochemical properties of nucleotides into the pseudo K-tuple nucleotide composition (PseKNC), we proposed a powerful predictor called 2L-piRNA. It is a two-layer ensemble classifier, in which the first layer is for identifying whether a query RNA molecule is piRNA or non-piRNA, and the second layer for identifying whether a piRNA is with or without the function of instructing target mRNA deadenylation. Rigorous cross-validations have indicated that the success rates achieved by the proposed predictor are quite high. For the convenience of most biologists and drug development scientists, the web server for 2L-piRNA has been established at http://bioinformatics.hitsz.edu.cn/2L-piRNA/, by which users can easily get their desired results without the need to go through the mathematical details. |
| first_indexed | 2024-12-12T16:50:15Z |
| format | Article |
| id | doaj.art-6829915d42da4f8292efce97b55361ae |
| institution | Directory Open Access Journal |
| issn | 2162-2531 |
| language | English |
| last_indexed | 2024-12-12T16:50:15Z |
| publishDate | 2017-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj.art-6829915d42da4f8292efce97b55361ae2022-12-22T00:18:23ZengElsevierMolecular Therapy: Nucleic Acids2162-25312017-06-017C26727710.1016/j.omtn.2017.04.0082L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their FunctionBin Liu0Fan Yang1Kuo-Chen Chou2School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, ChinaSchool of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, ChinaGordon Life Science Institute, Belmont, MA 02478, USAInvolved with important cellular or gene functions and implicated with many kinds of cancers, piRNAs, or piwi-interacting RNAs, are of small non-coding RNA with around 19–33 nt in length. Given a small non-coding RNA molecule, can we predict whether it is of piRNA according to its sequence information alone? Furthermore, there are two types of piRNA: one has the function of instructing target mRNA deadenylation, and the other does not. Can we discriminate one from the other? With the avalanche of RNA sequences emerging in the postgenomic age, it is urgent to address the two problems for both basic research and drug development. Unfortunately, to the best of our knowledge, so far no computational methods whatsoever could be used to deal with the second problem, let alone deal with the two problems together. Here, by incorporating the physicochemical properties of nucleotides into the pseudo K-tuple nucleotide composition (PseKNC), we proposed a powerful predictor called 2L-piRNA. It is a two-layer ensemble classifier, in which the first layer is for identifying whether a query RNA molecule is piRNA or non-piRNA, and the second layer for identifying whether a piRNA is with or without the function of instructing target mRNA deadenylation. Rigorous cross-validations have indicated that the success rates achieved by the proposed predictor are quite high. For the convenience of most biologists and drug development scientists, the web server for 2L-piRNA has been established at http://bioinformatics.hitsz.edu.cn/2L-piRNA/, by which users can easily get their desired results without the need to go through the mathematical details.http://www.sciencedirect.com/science/article/pii/S2162253117301580non-coding RNApiRNAmRNA deadenylationcancersphysicochemical propertiesPseKNCweb server |
| spellingShingle | Bin Liu Fan Yang Kuo-Chen Chou 2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function Molecular Therapy: Nucleic Acids non-coding RNA piRNA mRNA deadenylation cancers physicochemical properties PseKNC web server |
| title | 2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function |
| title_full | 2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function |
| title_fullStr | 2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function |
| title_full_unstemmed | 2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function |
| title_short | 2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function |
| title_sort | 2l pirna a two layer ensemble classifier for identifying piwi interacting rnas and their function |
| topic | non-coding RNA piRNA mRNA deadenylation cancers physicochemical properties PseKNC web server |
| url | http://www.sciencedirect.com/science/article/pii/S2162253117301580 |
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