Trends in the development of miRNA bioinformatics tools

Abstract 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, structu...

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Vydané v:Briefings in bioinformatics Ročník 20; číslo 5; s. 1836 - 1852
Hlavní autori: Chen, Liang, Heikkinen, Liisa, Wang, Changliang, Yang, Yang, Sun, Huiyan, Wong, Garry
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Oxford University Press 27.09.2019
Oxford Publishing Limited (England)
Predmet:
Algorithms
Bioinformatics
Computational Biology - methods
Data mining
Epigenetics
Gene expression
Machine Learning
MicroRNAs
MicroRNAs - chemistry
MicroRNAs - genetics
miRNA
Network analysis
Nucleic Acid Conformation
Predictions
Review
Ribonucleic acid
RNA
Target recognition
Trends
bibliometric
miRNA
text mining
ranking
bioinformatics tools
ISSN:1467-5463, 1477-4054, 1477-4054
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Shrnutí:Abstract 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.
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ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bby054