Mapping putative microRNA target sites and conserved RNA motifs among interacting genes

  Non-coding RNAs play a huge role in regulation of gene expression in nearly all organisms examined so far.  A prevailing class of non-coding RNA is microRNA (miRNA) which regulates a wide range of cellular behaviors in both animals and plants.  One obstacle toward the understanding of role of vast miRNAs is the accurate prediction of miRNA targets.  Despite years of development, current miRNA-target prediction algorithms are still far from perfect.  We wish to propose another algorithm to predict miRNA targets based on the analysis of the 3' untranslated region (UTR) sequences of all genes in a given pathway.  We also want to ask a fundamental question: do interacting genes tend to share cis-acting RNA elements?

Sub-project 1: Mapping putative microRNA target sites in known pathways (PathTar)
 
Sub-project 2: Test if interacting genes tend to share conserved RNA motifs
(CoMotif)


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