MicroRNA Databases and Tools

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2021 Aug 25

PMID 34432277

Citations 3

Authors

Tharcisio Soares de Amorim

Daniel Longhi Fernandes Pedro

Alexandre Rossi Paschoal

Affiliations

Soon will be listed here.

Abstract

In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.

Citing Articles

The Role of microRNAs in Epigenetic Regulation of Signaling Pathways in Neurological Pathologies.

Tregub P, Ibrahimli I, Averchuk A, Salmina A, Litvitskiy P, Manasova Z Int J Mol Sci. 2023; 24(16).

PMID: 37629078 PMC: 10454825. DOI: 10.3390/ijms241612899.

Integrated analysis of lncRNAs, mRNAs, and TFs to identify network modules underlying diterpenoid biosynthesis in .

Wang L, Zou P, Liu F, Liu R, Yan Z, Chen X PeerJ. 2023; 11:e15332.

PMID: 37187524 PMC: 10178227. DOI: 10.7717/peerj.15332.

wTAM: a web server for annotation of weighted human microRNAs.

Cui C, Fan R, Zhou Y, Cui Q Bioinform Adv. 2023; 2(1):vbab040.

PMID: 36699401 PMC: 9710651. DOI: 10.1093/bioadv/vbab040.

References

Paschoal A, Maracaja-Coutinho V, Setubal J, Simoes Z, Verjovski-Almeida S, Durham A . Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases. RNA Biol. 2012; 9(3):274-82. DOI: 10.4161/rna.19352. View

Kozomara A, Birgaoanu M, Griffiths-Jones S . miRBase: from microRNA sequences to function. Nucleic Acids Res. 2018; 47(D1):D155-D162. PMC: 6323917. DOI: 10.1093/nar/gky1141. View

Maracaja-Coutinho V, Paschoal A, Caris-Maldonado J, Borges P, Ferreira A, Durham A . Noncoding RNAs Databases: Current Status and Trends. Methods Mol Biol. 2019; 1912:251-285. DOI: 10.1007/978-1-4939-8982-9_10. View

Singh N . microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations. Interdiscip Sci. 2016; 9(3):357-377. DOI: 10.1007/s12539-016-0166-7. View

Lee R, Feinbaum R, Ambros V . The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993; 75(5):843-54. DOI: 10.1016/0092-8674(93)90529-y. View

Lukasik A, Wojcikowski M, Zielenkiewicz P . Tools4miRs - one place to gather all the tools for miRNA analysis. Bioinformatics. 2016; 32(17):2722-4. PMC: 5013900. DOI: 10.1093/bioinformatics/btw189. View

Da Fonseca B, Silva Domingues D, Paschoal A . mirtronDB: a mirtron knowledge base. Bioinformatics. 2019; 35(19):3873-3874. PMC: 6761972. DOI: 10.1093/bioinformatics/btz153. View

Ma X, Liu C, Gu L, Mo B, Cao X, Chen X . TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants. Bioinformatics. 2017; 34(9):1574-1576. PMC: 6248703. DOI: 10.1093/bioinformatics/btx797. View

Li J, Han X, Wan Y, Zhang S, Zhao Y, Fan R . TAM 2.0: tool for MicroRNA set analysis. Nucleic Acids Res. 2018; 46(W1):W180-W185. PMC: 6031048. DOI: 10.1093/nar/gky509. View

10.

Kaushik A, Saraf S, Mukherjee S, Gupta D . miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. PeerJ. 2015; 3:e1332. PMC: 4662591. DOI: 10.7717/peerj.1332. View

11.

Corrada D, Viti F, Merelli I, Battaglia C, Milanesi L . myMIR: a genome-wide microRNA targets identification and annotation tool. Brief Bioinform. 2011; 12(6):588-600. DOI: 10.1093/bib/bbr062. View

12.

Artzi S, Kiezun A, Shomron N . miRNAminer: a tool for homologous microRNA gene search. BMC Bioinformatics. 2008; 9:39. PMC: 2258288. DOI: 10.1186/1471-2105-9-39. View

13.

Barenboim M, Zoltick B, Guo Y, Weinberger D . MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum Mutat. 2010; 31(11):1223-32. PMC: 3001138. DOI: 10.1002/humu.21349. View

14.

Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, Romualdi C . MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. Nucleic Acids Res. 2010; 38(Web Server issue):W352-9. PMC: 2896126. DOI: 10.1093/nar/gkq423. View

15.

Bartonicek N, Enright A . SylArray: a web server for automated detection of miRNA effects from expression data. Bioinformatics. 2010; 26(22):2900-1. DOI: 10.1093/bioinformatics/btq545. View

16.

Higashi S, Fournier C, Gautier C, Gaspin C, Sagot M . Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. BMC Bioinformatics. 2015; 16:179. PMC: 4448272. DOI: 10.1186/s12859-015-0594-0. View

17.

Bonnet E, He Y, Billiau K, Van de Peer Y . TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics. 2010; 26(12):1566-8. DOI: 10.1093/bioinformatics/btq233. View

18.

LYi S, Jung D, Oh M, Kim B, Freishtat R, Giri M . miRTarVis+: Web-based interactive visual analytics tool for microRNA target predictions. Methods. 2017; 124:78-88. DOI: 10.1016/j.ymeth.2017.06.004. View

19.

Tong Y, Ru B, Zhang J . miRNACancerMAP: an integrative web server inferring miRNA regulation network for cancer. Bioinformatics. 2018; 34(18):3211-3213. DOI: 10.1093/bioinformatics/bty320. View

20.

Hamed M, Spaniol C, Nazarieh M, Helms V . TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. Nucleic Acids Res. 2015; 43(W1):W283-8. PMC: 4489273. DOI: 10.1093/nar/gkv418. View