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Algoritem za detekcijo komponent kompleksov proteinov v interakciji z RNA
ID SPASIĆ, MILUTIN (Author), ID Curk, Tomaž (Mentor) More about this mentor... This link opens in a new window, ID Ule, Jernej (Co-mentor)

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MD5: 95DD5B9AA5100583BB6C11CD6BD1AAE2
PID: 20.500.12556/rul/0022ad41-83e9-4d9b-ba8a-801e5ff40a7e

Abstract
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
Work type:Bachelor thesis/paper (mb11)
Organization:FRI - Faculty of computer and information science
Year:2014
PID:20.500.12556/RUL-29479 This link opens in a new window
Publication date in RUL:17.09.2014
Views:1103
Downloads:470
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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

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