20.500.12556/RUL-29479 Algoritem za detekcijo komponent kompleksov proteinov v interakciji z RNA diplomsko delo Algorithm for detecting components of ribonucleoprotein complexes 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. 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. interakcije protein-RNA faktorizacija nenegativnih matrik iCLIP kompleksi proteinov in RNA ačunalništvo računalništvo in informatika univerzitetni študij diplomske naloge protein-RNA interactions nonnegative matrix factorization iCLIP protein complexes computer science computer and information science diploma true false false [M. Spasić] Slovenski jezik Angleški jezik Diplomsko delo/naloga 2014-09-17 14:45:01 2014-09-17 14:45:01 2024-08-12 14:59:09 0000-00-00 00:00:00 2014 0 0 50 str. 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 14209 1536122307 63110397-20140912085338-spasicm.pdf 63110397-20140912085338-spasicm.pdf 1 95DD5B9AA5100583BB6C11CD6BD1AAE2 7beced7b0e70abd8ce477b4737ca9a2c46ece4541536761fe8228af91827decd 4b0de155-a1a8-11eb-a523-00155dcfd717 20.500.12556/rul/0022ad41-83e9-4d9b-ba8a-801e5ff40a7e https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=29474 Fakulteta za računalništvo in informatiko 0 0 0