Algoritem za detekcijo komponent kompleksov proteinov v interakciji z RNA : diplomsko delo

SPASIĆ, MILUTIN (author), Curk, Tomaž (mentor), Ule, Jernej (comentor)

Proteini so pomembni akterji v mnogih celičnih procesih. Interakcije proteinov in RNA imajo pomembno vlogo pri uravnavanju izražanja genov in posledično njihove funkcije. V interakcijo z RNA navadno vstopa več tako posameznih proteinov kakor tudi skupin proteinov. Metoda iCLIP omogoča do nukleotida natančno detekcijo mest interakcij na RNA z izbranim proteinom. V diplomskem delu smo razvili metodo, ki sprejme nabor mest na RNA, ki so v interakciji z izbranim proteinskim kompleksom. V okolici teh mest nato poišče vzorce interakcij iz nabora interakcij proteinov z RNA, za katere imamo podatke. Najdeni vzorci vključujejo tako posamezne komponente (proteine) danega kompleksa kakor tudi proteine, ki danega kompleksa ne tvorijo, ampak vseeno vplivajo na interakcije kompleksa z RNA. Razvita metoda temelji na postopeku faktorizacije nenegativnih matrik. Metodo smo uspešno preizkusili na podatkih o kompleksu SmB, kjer smo uspešno določiti nekaj proteinov, ki so soudeleženi v kompleksu SmB.

• Language: Slovenian
• Keywords: interakcije protein-RNA, faktorizacija nenegativnih matrik, iCLIP, kompleksi proteinov in RNA, ačunalništvo, računalništvo in informatika, univerzitetni študij, diplomske naloge
• Work type: Bachelor thesis/paper
• Typology: 2.11 - Undergraduate Thesis
• Organization: FRI - Faculty of Computer and Information Science
• Publisher: [M. Spasić]
• Year: 2014
• Number of pages: 50 str.
• PID: 20.500.12556/RUL-29479
• COBISS.SI-ID: 1536122307
• Publication date in RUL: 17.09.2014

Secondary language

• Language: English
• Title: Algorithm for detecting components of ribonucleoprotein complexes

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.

• Keywords: protein-RNA interactions, nonnegative matrix factorization, iCLIP, protein complexes, computer science, computer and information science, diploma