Predicting Interactions between microRNAs and mRNA

Status: selected

Praktikum (Bachelor/Master)

Field: Gene/MicroRNA expression/regulation

Advisors: Rehberg, Engelmann

Courses Required: Practical Bioinformatics I, good R programming skills

Objective: microRNAs (miRNAs) are short RNAs (~21-24 nt) which can bind to other mRNAs and regulate their abundances and thus affect various biological processes. Modern high-throughput technologies, allow to detect the paired expression of many RNAs and miRNAs. For paired expression profiles it was shown that by using a least angle regression approach the gene expression could be reconstructed from the miRNA expression and new interactions which can be associated with cancer [1] discovered. In this project, the approach described in [1] should be applied on newer and larger miRNA-mRNA datasets and the results compared to the previous outcomes.

First-Steps: Get familiar with the data preprocessing steps and interaction modeling with regression algorithms.

Questions: Can the previous results be confirmed on new data? What are the regulation targets of the miRNAs in these datasets?

Start Reading:

[1] "A Least Angle Regression Model for the Prediction of Canonical and Non-Canonical miRNA-mRNA Interactions" Julia C. Engelmann, Rainer Spang (2012) PLoS ONE; journals.plos.org/plosone/article