Publication Details

In silico search for secondary structures in p53 target genes using R/Bioconductor

BRÁZDOVÁ Marie, MARTÍNEK Tomáš and LEXA Matej. In silico search for secondary structures in p53 target genes using R/Bioconductor. In: ITAT 2013: Information Technologies - Applications and Theory. Donovaly: CreativeSpace Independent Publishing Platform, 2013, pp. 42-46. ISBN 978-1-4909-5208-6.
Czech title
Vyhledávání sekundárních struktur v cílových genech proteinu p53 s využitím prostředí R/Bioconductor
Type
conference paper
Language
english
Authors
Brázdová Marie, Mgr., Ph.D. (IBP)
Martínek Tomáš, doc. Ing., Ph.D. (DCSY FIT BUT)
Lexa Matej, Ing., Ph.D. (FI MUNI)
Keywords

R/bioconductor; p53; bioinformatics; DNA sequence analysis

Abstract

p53 is a well-known transcription factor and tumor suppressor, regulating among other processes, the commitment of cells to apoptosis and DNA repair. p53 mutants are often found in cancers of different kinds, either as mutant or misregulated p53. p53 is involved in many other processes and we currently do not understand the full range of its functions. It is known to recognize the p53con sequence by its specific DNA-binding domain (DBD). It is also known to bind DNA non-specifically. This binding has been shown to involve superhelical DNA, more specifically, cruciform, triplex and quadruplex structures. In our laboratories we were intrigued by the possible interplay between non-canonical DNA structure binding and regular p53con binding. In an attempt to clarify this interplay and discover suitable candidate genes for further study, we carried out an in silico study on the human genome. We identified all the occurences of potential cruciform DNA, triplex DNA, quadruplex DNA and p53con recognition sequences in +/-40000 bp regions of known genes. We analyzed this data for statistically significant patterns and combinations of patterns using a small set of available R/Bioconductor packages. This paper describes the computational pipeline designed for this type of studies. We also show preliminary results for selected human sequences.

Published
2013
Pages
42-46
Proceedings
ITAT 2013: Information Technologies - Applications and Theory
Conference
Information Technology - Applications and Theory, Hotel Zornička, Donovaly, SK
ISBN
978-1-4909-5208-6
Publisher
CreativeSpace Independent Publishing Platform
Place
Donovaly, SK
BibTeX 
@INPROCEEDINGS{FITPUB10455,
   author = "Marie Br\'{a}zdov\'{a} and Tom\'{a}\v{s} Mart\'{i}nek and Matej Lexa",
   title = "In silico search for secondary structures in p53 target genes using R/Bioconductor",
   pages = "42--46",
   booktitle = "ITAT 2013: Information Technologies - Applications and Theory",
   year = 2013,
   location = "Donovaly, SK",
   publisher = "CreativeSpace Independent Publishing Platform",
   ISBN = "978-1-4909-5208-6",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/10455"
}
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