Abstract
MicroRNAs (miRNAs) are short RNA sequences actively involved in post-transcriptional gene regulation. Such miRNAs have been discovered in most eukaryotic organisms. They also seem to exist in viruses and perhaps in microbial pathogens to target the host. Drosha is the enzyme which first cleaves the pre-miRNA from the nascent pri-miRNA. Previously, we showed that it is possible to distinguish between pre-miRNAs of different species depending on their evolutionary distance using just k-mers.
In this study, we introduce three new sets of features which are extracted from the precursor sequence and summarize the distance between k-mers. These new set of features, named inter k-mer distance, k-mer location distance and k-mer first-last distance, were compared to k-mer and all other published features describing a pre-miRNA. Classification at well above 80% (depending on the evolutionary distance) is possible with a combination of distance and regular k-mer features.
The novel features specifically aid classification at closer evolutionary distances when compared to k-mers only. K-mer and k-mer distance features together lead to accurate classification for larger evolutionary distances such as Homo sapiens versus Brassicaceae (93% ACC). Including the novel distance features further increases the average accuracy since they are more effective for lower evolutionary distances. Secondary structure-based features were not effective in this study. We hope that this will fuel further analysis of miRNA evolution. Additionally, our approach provides another line of evidence when predicting pre-miRNAs and can be used to ensure that miRNAs detected in NGS samples are indeed not contaminations. In the future, we aim for automatic categorization of unknown hairpins into all species/clades available in miRBase.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Allmer, J., Yousef, M.: Computational methods for ab initio detection of microRNAs. Front. Genet. 3, 209 (2012). https://doi.org/10.3389/fgene.2012.00209
Berthold, M.R., Cebron, N., Dill, F., et al.: KNIME: the Konstanz information miner. In: Preisach, C., Burkhardt, H., Schmidt-Thime, L., Decker, R. (eds.) Data Analysis, Machine Learning and Applications, pp. 319–326. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-78246-9_38
Chapman, E.J., Carrington, J.C.: Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8(11), 884–896 (2007). https://doi.org/10.1038/nrg2179
Dang, H.T., Tho, H.P., Satou, K., Tu, B.H.: Prediction of microRNA hairpins using one-class support vector machines. In: 2nd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2008, pp. 33–36 (2008)
Edgar, R.C.: Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19), 2460–2461 (2010). https://doi.org/10.1093/bioinformatics/btq461
Erson-Bensan, A.E.: Introduction to MicroRNAs in biological systems. In: Yousef, M., Allmer, J. (eds.) miRNomics: MicroRNA Biology and Computational Analysis, 1st edn. Humana Press, New York, pp. 1–14 (2014)
Fromm, B., Billipp, T., Peck, L.E., et al.: A uniform system for the annotation of vertebrate microRNA genes and the evolution of the human microRNAome. Annu. Rev. Genet. 49, 213–242 (2015). https://doi.org/10.1146/annurev-genet-120213-092023
Grey, F.: Role of microRNAs in herpesvirus latency and persistence. J. Gen. Virol. 96(4), 739–751 (2015). https://doi.org/10.1099/vir.0.070862-0
Griffiths-Jones, S.: miRBase: microRNA sequences and annotation. Curr. Protoc. Bioinf. 12.9.1–12.9.10 (2010). Chap. 12. Unit. https://doi.org/10.1002/0471250953.bi1209s29
Hsu, S.-D., Tseng, Y.-T., Shrestha, S., et al.: miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 42(Database issue), D78–D85 (2014). https://doi.org/10.1093/nar/gkt1266
Khalifa, W., Yousef, M., Saçar Demirci, M.D., Allmer, J.: The impact of feature selection on one and two-class classification performance for plant microRNAs. PeerJ 4, e2135 (2016). https://doi.org/10.7717/peerj.2135
Kozomara, A., Griffiths-Jones, S.: miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39(Database issue), D152–D157 (2011). https://doi.org/10.1093/nar/gkq1027
Lai, E.C., Tomancak, P., Williams, R.W., Rubin, G.M.: Computational identification of Drosophila microRNA genes. Genome Biol. 4(7), R42 (2003). https://doi.org/10.1186/gb-2003-4-7-r42
Matthews, B.W.: Comparison of the predicted and observed secondary structure of T4 phage lysozyme. BBA - Protein Struct. 405(2), 442–451 (1975). https://doi.org/10.1016/0005-2795(75)90109-9
Saçar Demirci, M.D., Baumbach, J., Allmer, J.: On the performance of pre-microRNA detection algorithms. Nat. Commun. (2017). https://doi.org/10.1038/s41467-017-00403-z
Saçar Demirci, M.D., Allmer, J.: Data mining for microRNA gene prediction: on the impact of class imbalance and feature number for microrna gene prediction. In: 2013 8th International Symposium on Health Informatics and Bioinformatics, pp. 1–6. IEEE (2013)
Saçar Demirci, M.D., Allmer, J.: Machine learning methods for MicroRNA gene prediction. In: Yousef, M., Allmer, J. (eds.) miRNomics: MicroRNA Biology and Computational Analysis SE - 10, 1st edn., pp. 177–187. Humana Press, New York (2014)
Vergoulis, T., Vlachos, I.S., Alexiou, P., et al.: TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res. 40(Database issue), D222–D229 (2012). https://doi.org/10.1093/nar/gkr1161
Xu, Q.-S., Liang, Y.-Z.: Monte Carlo cross validation. Chemom. Intell. Lab. Syst. 56(1), 1–11 (2001). https://doi.org/10.1016/S0169-7439(00)00122-2
Yones, C.A., Stegmayer, G., Kamenetzky, L., Milone, D.H.: miRNAfe: a comprehensive tool for feature extraction in microRNA prediction. Biosystems 138, 1–5 (2015). https://doi.org/10.1016/j.biosystems.2015.10.003
Yousef, M., Allmer, J., Khalifa, W.: Plant microRNA prediction employing sequence motifs achieves high accuracy (2016)
Yousef, M., Jung, S., Showe, L.C., Showe, M.K.: Learning from positive examples when the negative class is undetermined–microRNA gene identification. Algorithms Mol. Biol. 3, 2 (2008). https://doi.org/10.1186/1748-7188-3-2
Yousef, M., Khalifa, W., Acar, I.E., Allmer, J.: MicroRNA categorization using sequence motifs and k-mers. BMC Bioinf. 18(1), 170 (2017a). https://doi.org/10.1186/s12859-017-1584-1
Yousef, M., Nebozhyn, M., Shatkay, H., et al.: Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier. Bioinformatics 22(11), 1325–1334 (2006). https://doi.org/10.1093/bioinformatics/btl094
Yousef, M., Nigatu, D., Levy, D., et al.: Categorization of species based on their MicroRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers. EURASIP J. Adv. Sig. Process. 2017(70), 1–10 (2017b). https://doi.org/10.1186/s13634-017-0506-8
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this paper
Cite this paper
Yousef, M., Allmer, J. (2019). Classification of Pre-cursor microRNAs from Different Species Using a New Set of Features. In: Anderst-Kotsis, G., et al. Database and Expert Systems Applications. DEXA 2019. Communications in Computer and Information Science, vol 1062. Springer, Cham. https://doi.org/10.1007/978-3-030-27684-3_3
Download citation
DOI: https://doi.org/10.1007/978-3-030-27684-3_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-27683-6
Online ISBN: 978-3-030-27684-3
eBook Packages: Computer ScienceComputer Science (R0)