In silico search for secondary structures in p53 target genes using R/Bioconductor
Identifikátory výsledku
Kód výsledku v 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>
Výsledek na webu
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DOI - Digital Object Identifier
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Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
In silico search for secondary structures in p53 target genes using R/Bioconductor
Popis výsledku v původním jazyce
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.
Název v anglickém jazyce
In silico search for secondary structures in p53 target genes using R/Bioconductor
Popis výsledku anglicky
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.
Klasifikace
Druh
D - Stať ve sborníku
CEP obor
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OECD FORD obor
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Návaznosti výsledku
Projekt
<a href="/cs/project/ED1.1.00%2F02.0070" target="_blank" >ED1.1.00/02.0070: Centrum excelence IT4Innovations</a><br>
Návaznosti
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
Ostatní
Rok uplatnění
2013
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Údaje specifické pro druh výsledku
Název statě ve sborníku
ITAT 2013: Information Technologies - Applications and Theory
ISBN
978-1-4909-5208-6
ISSN
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e-ISSN
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Počet stran výsledku
5
Strana od-do
42-46
Název nakladatele
CreativeSpace Independent Publishing Platform
Místo vydání
Donovaly
Místo konání akce
Hotel Zornička, Donovaly
Datum konání akce
11. 9. 2013
Typ akce podle státní příslušnosti
EUR - Evropská akce
Kód UT WoS článku
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