Title

Discovering Non-Coding Rna Elements In Drosophila 3′ Untranslated Regions

Keywords

3′ untranslated region; Bioinformatics; Clustering; Drosophila genome; Non-coding RNA; Post-transcriptional regulation; RNA secondary structure

Abstract

The Non-Coding RNA (ncRNA) elements in the 3′ Untranslated Regions (3′-UTRs) are known to participate in the genes' post-transcriptional regulations. Inferring co-expression patterns of the genes through clustering these 3′-UTR ncRNA elements will provide invaluable insights for studying their biological functions. In this paper, we propose an improved RNA structural clustering pipeline. Benchmark of the new pipeline on Rfam data demonstrates over 10% performance improvements compared to the traditional hierarchical clustering pipeline. By applying the new clustering pipeline to 3′-UTRs of Drosophila melanogaster's genome, we have successfully identified 184 ncRNA clusters with 91.3% accuracy. One of these clusters corresponds to genes that are preferentially expressed in male Drosophila. Another cluster contains genes that are responsible for the functions of septate junction in epithelial cells. These discoveries encourage more studies on novel post-transcriptional regulation mechanisms. Copyright © 2014 Inderscience Enterprises Ltd.

Publication Date

1-1-2014

Publication Title

International Journal of Bioinformatics Research and Applications

Volume

10

Issue

4-5

Number of Pages

479-497

Document Type

Article

Personal Identifier

scopus

DOI Link

https://doi.org/10.1504/IJBRA.2014.062996

Socpus ID

84904022761 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/84904022761

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