Milutin Spasić (2014) Algorithm for detecting components of ribonucleoprotein complexes. EngD thesis.
Abstract
Proteins play an important role in many processes in a cell. Protein-RNA interactions greatly affect the balancing of gene expressions and consequently their functions. Interaction with RNA may occur with a single protein or a protein complex. iCLIP method is able to detect the protein-RNA crosslink spots with nucleotide resolution. We developed a method that takes a set of crosslink spots that intersect with the choosen protein complex as an input. Method is searching the crosslink spots neighbourhood for the protein-RNA interaction patterns. Found patterns include parts (proteins) of the choosen complex and other proteins that are not a part of the choosen complex, but still affect the interactions of the choosen complex with the RNA. Method that we developed is based on the non-negative matrix factorization. We successfully tested the method on a SmB complex where we found a few proteins that cooporate with SmB complex.
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