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Algorithm for detecting components of ribonucleoprotein complexes

Milutin Spasić (2014) Algorithm for detecting components of ribonucleoprotein complexes. EngD thesis.

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    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.

    Item Type: Thesis (EngD thesis)
    Keywords: protein-RNA interactions, nonnegative matrix factorization, iCLIP, protein complexes
    Number of Pages: 50
    Language of Content: Slovenian
    Mentor / Comentors:
    Name and SurnameIDFunction
    doc. dr. Tomaž Curk299Mentor
    Link to COBISS: http://www.cobiss.si/scripts/cobiss?command=search&base=51012&select=(ID=1536122307)
    Institution: University of Ljubljana
    Department: Faculty of Computer and Information Science
    Item ID: 2670
    Date Deposited: 12 Sep 2014 16:26
    Last Modified: 18 Dec 2014 11:42
    URI: http://eprints.fri.uni-lj.si/id/eprint/2670

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