Abstract
microRNAs (miRNAs) are central regulators of gene expression. They are actively studied for their involvement in numerous physiological and pathological conditions but also as diagnostic biomarkers or promising therapeutic targets. The increased complexity of the miRNA interactomes hinders straightforward interpretation of miRNA expression differences between states and conditions. To this end, functional analysis web servers process and combine experimental and in silico data, enabling researchers to uncover targeted pathways and transcriptional mechanisms that are hidden within numerous interactions and vast expression datasets. DIANA-tools (www.microrna.gr) is a web server hosting state-of-the-art utilities and databases for miRNA functional investigation. Available utilities cover a wide scope of different needs and research scenarios, rendering DIANA website a one-stop-shop for miRNA analyses. The most commonly utilized databases and algorithms include DIANA-microT-CDS, DIANA-TarBase v7.0, DIANA-lncBase v2.0, DIANA-miRGen v3.0, DIANA-miRPath v3.0, and DIANA-mirExTra v2.0.
In the presented protocol, we will utilize different online tools in order to explore miRNA functions and to identify probable targets of interest for downstream analyses and wet lab experiments. The combined use of different applications from the DIANA suite can shed light to numerous different aspects of miRNA regulation and regulatory function, without the necessity for extensive bioinformatics expertise or computational infrastructure.
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References
Vlachos IS, Hatzigeorgiou AG (2013) Online resources for miRNA analysis. Clin Biochem 46(10-11):879–900. doi:10.1016/j.clinbiochem.2013.03.006
Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, Hatzigeorgiou AG (2010) The DIANA-mirExTra web server: from gene expression data to MicroRNA function. PLoS One 5(2), e9171. doi:10.1371/journal.pone.0009171
Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I, Anastasopoulos IL, Maniou S, Karathanou K, Kalfakakou D, Fevgas A, Dalamagas T, Hatzigeorgiou AG (2015) DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res 43(Database issue):D153–D159. doi:10.1093/nar/gku1215
Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG (2013) DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res 41(Web Server Issue):W169–W173
Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, Zagganas K, Tsanakas P, Floros E, Dalamagas T, Hatzigeorgiou AG (2016) DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res 44(D1):D231–D238. doi:10.1093/nar/gkv1270
Georgakilas G, Vlachos IS, Zagganas K, Vergoulis T, Paraskevopoulou MD, Kanellos I, Tsanakas P, Dellis D, Fevgas A, Dalamagas T, Hatzigeorgiou AG (2016) DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Res 44(D1):D190–D195. doi:10.1093/nar/gkv1254
Vlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, Vergoulis T, Dalamagas T, Hatzigeorgiou AG (2015) DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Res 2015:gkv403. doi:10.1093/nar/gkv403
Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18(10):1165–1178. doi:10.1101/gad.1184704
Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG (2014) MicroTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat Commun 5:5700. doi:10.1038/ncomms6700
Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 18(10):1139–1146. doi:10.1038/nsmb.2115
Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42(D1):D68–D73. doi:10.1093/nar/gkt1181
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A (2013) NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res 41(Database issue):D991–D995. doi:10.1093/nar/gks1193
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ (2015) The UCSC genome browser database: 2015 update. Nucleic Acids Res 43(Database issue):D670–D681. doi:10.1093/nar/gku1177
Consortium EP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74. doi:10.1038/nature11247
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10):R106. doi:10.1186/gb-2010-11-10-r106
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43(7):47. doi:10.1093/nar/gkv007
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140. doi:10.1093/bioinformatics/btp616
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Giron CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, Flicek P (2016) Ensembl 2016. Nucleic Acids Res 44(D1):D710–D716. doi:10.1093/nar/gkv1157
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42(Database issue):D199–D205. doi:10.1093/nar/gkt1076
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25(1):25–29. doi:10.1038/75556
Acknowledgments
The authors would like to thank Maria D. Paraskevopoulou, Dimitra Karagkouni, and Georgios Georgakilas for their helpful comments and suggestions.
This work has been supported from the project “NGS-infect” from Greek General Secretary of Research and Technology.
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Vlachos, I.S., Hatzigeorgiou, A.G. (2017). Functional Analysis of miRNAs Using the DIANA Tools Online Suite. In: Schmidt, M. (eds) Drug Target miRNA. Methods in Molecular Biology, vol 1517. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6563-2_2
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DOI: https://doi.org/10.1007/978-1-4939-6563-2_2
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