Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Chen, Liang, Heikkinen, Liisa, Wang, Changliang, Yang, Yang, Sun, Huiyan, Wong, Garry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
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
_version_ 1783568984800493568
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
work_keys_str_mv AT chenliang trendsinthedevelopmentofmirnabioinformaticstools
AT heikkinenliisa trendsinthedevelopmentofmirnabioinformaticstools
AT wangchangliang trendsinthedevelopmentofmirnabioinformaticstools
AT yangyang trendsinthedevelopmentofmirnabioinformaticstools
AT sunhuiyan trendsinthedevelopmentofmirnabioinformaticstools
AT wonggarry trendsinthedevelopmentofmirnabioinformaticstools