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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26230%2F13%3APU106432" target="_blank" >RIV/00216305:26230/13:PU106432 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

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

Original language description

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.

Czech name

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Czech description

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Type

D - Article in proceedings

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/ED1.1.00%2F02.0070" target="_blank" >ED1.1.00/02.0070: IT4Innovations Centre of Excellence</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)<br>S - Specificky vyzkum na vysokych skolach

Publication year

2013

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection

ITAT 2013: Information Technologies - Applications and Theory

ISBN

978-1-4909-5208-6

ISSN

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e-ISSN

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Number of pages

5

Pages from-to

42-46

Publisher name

CreativeSpace Independent Publishing Platform

Place of publication

Donovaly

Event location

Hotel Zornička, Donovaly

Event date

Sep 11, 2013

Type of event by nationality

EUR - Evropská akce

UT code for WoS article

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