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. 2016 Mar 24:6:23700.
doi: 10.1038/srep23700.

miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels

Li Guo  1 , Jiafeng Yu  2 , Tingming Liang  3 , Quan Zou  4
Affiliations

miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels

Li Guo et al. Sci Rep. .

Abstract

MicroRNA (miRNA) locus has been found that can generate a series of varied isomiR sequences. Most studies always focus on determining miRNA level, however, the canonical miRNA sequence is only a specific member in the multiple isomiRs. Some studies have shown that isomiR sequences play versatile roles in biological progress, and the analysis and research should be simultaneously performed at the miRNA/isomiR levels. Based on the biological characteristics of miRNA and isomiR, we developed miR-isomiRExp to analyze expression pattern of miRNA at the miRNA/isomiR levels, provide insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveal functional characteristics of miRNA/isomiR. Simultaneously, we also performed expression analysis of specific human diseases using public small RNA sequencing datasets based on the analysis platform, which may help in surveying the potential deregulated miRNA/isomiR expression profiles, especially sequence and function-related isomiRs for further interaction analysis and study. The miR-isomiRExp platform provides miRNA/isomiR expression patterns and more information to study deregulated miRNA loci and detailed isomiR sequences. This comprehensive analysis will enrich experimental miRNA studies. miR-isomiRExp is available at http://mirisomirexp.aliapp.com.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Flowchart for the analysis of miRNA at the miRNA and isomiR levels.
Figure 2
Figure 2. Differentially expressed miRNA/isomiR species in diseased samples.
(A) The analysis pipeline; (B) The detailed screened result.
Figure 3
Figure 3. An example of the expression analysis of isomiR expression profiles in the let-7 gene family (including the isomiRs from miR-#-5p and miR-#-3p loci).
(A) Scatter-plots of log2(5p/3p) in abundantly expressed let-7 members; (B) Box plots of let-7 members based on the 5p and 3p arms, respectively;(C) Expression of the dominant isomiR types in breast cancer (BC) tissues and normal tissues.
Figure 4
Figure 4. KS-test plots of isomiR distributions in the 5p and 3p arms, respectively, in the hsa-let-7 gene family.
See this image and copyright information in PMC

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References

    1. Neilsen C. T., Goodall G. J. & Bracken C. P. IsomiRs-the overlooked repertoire in the dynamic microRNAome. Trends Genet 28, 544–549 (2012). - PubMed
    1. Guo L. & Chen F. A Challenge for miRNA: Multiple IsomiRs in miRNAomics. Gene 544, 1–7 (2014). - PubMed
    1. Morin R. D. et al.. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res 18, 571–584 (2008). - PMC - PubMed
    1. Morin R. D. et al.. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18, 610–621 (2008). - PMC - PubMed
    1. Guo L. et al.. A Comprehensive Survey of miRNA Repertoire and 3′ Addition Events in the Placentas of Patients with Pre-eclampsia from High-throughput Sequencing. PloS one 6, e21072 (2011). - PMC - PubMed

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