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Trends in the development of miRNA bioinformatics tools
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analy...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414524/ https://www.ncbi.nlm.nih.gov/pubmed/29982332 http://dx.doi.org/10.1093/bib/bby054 |
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author | Chen, Liang Heikkinen, Liisa Wang, Changliang Yang, Yang Sun, Huiyan Wong, Garry |
author_facet | Chen, Liang Heikkinen, Liisa Wang, Changliang Yang, Yang Sun, Huiyan Wong, Garry |
author_sort | Chen, Liang |
collection | PubMed |
description | MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools. |
format | Online Article Text |
id | pubmed-7414524 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-74145242020-08-12 Trends in the development of miRNA bioinformatics tools Chen, Liang Heikkinen, Liisa Wang, Changliang Yang, Yang Sun, Huiyan Wong, Garry Brief Bioinform Review Articles MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools. Oxford University Press 2019-06-17 /pmc/articles/PMC7414524/ /pubmed/29982332 http://dx.doi.org/10.1093/bib/bby054 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Review Articles Chen, Liang Heikkinen, Liisa Wang, Changliang Yang, Yang Sun, Huiyan Wong, Garry Trends in the development of miRNA bioinformatics tools |
title | Trends in the development of miRNA bioinformatics tools |
title_full | Trends in the development of miRNA bioinformatics tools |
title_fullStr | Trends in the development of miRNA bioinformatics tools |
title_full_unstemmed | Trends in the development of miRNA bioinformatics tools |
title_short | Trends in the development of miRNA bioinformatics tools |
title_sort | trends in the development of mirna bioinformatics tools |
topic | Review Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414524/ https://www.ncbi.nlm.nih.gov/pubmed/29982332 http://dx.doi.org/10.1093/bib/bby054 |
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