MiRTargetLink 2.0-interactive MiRNA Target Gene and Target Pathway Networks

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2021 May 19

PMID 34009375

Citations 73

Authors

Fabian Kern

Ernesto Aparicio-Puerta

Yongping Li

Tobias Fehlmann

Tim Kehl

Viktoria Wagner

Kamalika Ray

Nicole Ludwig

Hans-Peter Lenhof

Eckart Meese

Andreas Keller

Affiliations

Soon will be listed here.

Abstract

Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.

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References

Muniategui A, Nogales-Cadenas R, Vazquez M, Aranguren X, Agirre X, Luttun A . Quantification of miRNA-mRNA interactions. PLoS One. 2012; 7(2):e30766. PMC: 3279346. DOI: 10.1371/journal.pone.0030766. View

Giroux P, Bhajun R, Segard S, Picquenot C, Charavay C, Desquilles L . miRViz: a novel webserver application to visualize and interpret microRNA datasets. Nucleic Acids Res. 2020; 48(W1):W252-W261. PMC: 7319447. DOI: 10.1093/nar/gkaa259. View

Huang H, Lin Y, Li J, Huang K, Shrestha S, Hong H . miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database. Nucleic Acids Res. 2019; 48(D1):D148-D154. PMC: 7145596. DOI: 10.1093/nar/gkz896. View

Licursi V, Conte F, Fiscon G, Paci P . MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis. BMC Bioinformatics. 2019; 20(1):545. PMC: 6829817. DOI: 10.1186/s12859-019-3105-x. View

Fehlmann T, Backes C, Kahraman M, Haas J, Ludwig N, Posch A . Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs. Nucleic Acids Res. 2017; 45(15):8731-8744. PMC: 5587802. DOI: 10.1093/nar/gkx595. View

Seifer B, Su D, Taylor H . Circulating miRNAs in Murine Experimental Endometriosis. Reprod Sci. 2016; 24(3):376-381. DOI: 10.1177/1933719116667228. View

Hamberg M, Backes C, Fehlmann T, Hart M, Meder B, Meese E . MiRTargetLink--miRNAs, Genes and Interaction Networks. Int J Mol Sci. 2016; 17(4):564. PMC: 4849020. DOI: 10.3390/ijms17040564. View

Chen Z, Wang H, Zhong J, Yang J, Darwazeh R, Tian X . Significant changes in circular RNA in the mouse cerebral cortex around an injury site after traumatic brain injury. Exp Neurol. 2018; 313:37-48. DOI: 10.1016/j.expneurol.2018.12.003. View

Chen Y, Wang X . miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2019; 48(D1):D127-D131. PMC: 6943051. DOI: 10.1093/nar/gkz757. View

10.

Laczny C, Leidinger P, Haas J, Ludwig N, Backes C, Gerasch A . miRTrail--a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. BMC Bioinformatics. 2012; 13:36. PMC: 3352041. DOI: 10.1186/1471-2105-13-36. View

11.

Huntzinger E, Izaurralde E . Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet. 2011; 12(2):99-110. DOI: 10.1038/nrg2936. View

12.

Latta L, Ludwig N, Krammes L, Stachon T, Fries F, Mukwaya A . Abnormal neovascular and proliferative conjunctival phenotype in limbal stem cell deficiency is associated with altered microRNA and gene expression modulated by PAX6 mutational status in congenital aniridia. Ocul Surf. 2020; 19:115-127. DOI: 10.1016/j.jtos.2020.04.014. View

13.

Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N . High-performance web services for querying gene and variant annotation. Genome Biol. 2016; 17(1):91. PMC: 4858870. DOI: 10.1186/s13059-016-0953-9. View

14.

Kowarsch A, Preusse M, Marr C, Theis F . miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. RNA. 2011; 17(5):809-19. PMC: 3078731. DOI: 10.1261/rna.2474511. View

15.

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

16.

Kern F, Krammes L, Danz K, Diener C, Kehl T, Kuchler O . Validation of human microRNA target pathways enables evaluation of target prediction tools. Nucleic Acids Res. 2020; 49(1):127-144. PMC: 7797041. DOI: 10.1093/nar/gkaa1161. View

17.

Xie G, Xia M, Miao Y, Luo M, Zhang Q, Guo A . FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human. Bioinformatics. 2019; 36(8):2605-2607. DOI: 10.1093/bioinformatics/btz929. View

18.

Vlachos I, Zagganas K, Paraskevopoulou M, Georgakilas G, Karagkouni D, Vergoulis T . DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Res. 2015; 43(W1):W460-6. PMC: 4489228. DOI: 10.1093/nar/gkv403. View

19.

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

20.

Martyniuk C, Martinez R, Kostyniuk D, Mennigen J, Zubcevic J . Genetic ablation of bone marrow beta-adrenergic receptors in mice modulates miRNA-transcriptome networks of neuroinflammation in the paraventricular nucleus. Physiol Genomics. 2020; 52(4):169-177. PMC: 7191424. DOI: 10.1152/physiolgenomics.00001.2020. View