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.
Keywords: 3' Drosophila genome; RNA secondary structure; bioinformatics; clustering; co–expression patterns; gene expression; ncRNA clusters; non–coding RNA; post–transcriptional regulation; untranslated region.