Podrobný výpis o publikaci

AZPEITIA, Eugenio, Mariana BENITEZ, Pablo PADILLA-LONGORIA, Carlos ESPINOSA-SOTO a Elena R. ALVAREZ-BUYLLA. Dynamic network-based epistasis analysis: Boolean examples. Frontiers in Plant Science. Switzerland: Frontiers, 2011, roč. 2011, č. 2, s. "nestránkováno", 12 s. ISSN 1664-462X. Dostupné z: https://dx.doi.org/10.3389/fpls.2011.00092.

Další formáty: BibTeX LaTeX RIS

TY  - JOUR
ID  - 970254
AU  - Azpeitia, Eugenio - Benitez, Mariana - Padilla-Longoria, Pablo - Espinosa-Soto, Carlos - Alvarez-Buylla, Elena R.
PY  - 2011
TI  - Dynamic network-based epistasis analysis: Boolean examples
JF  - Frontiers in Plant Science
VL  - 2011
IS  - 2
SP  - "nestránkováno"
EP  - "nestránkováno"
PB  - Frontiers
SN  - 1664462X
KW  - Boolean network
KW  - dynamic model
KW  - epistasis
UR  - http://www.frontiersin.org/plant_genetics_and_genomics/10.3389/fpls.2011.00092/abstract
L2  - http://www.frontiersin.org/plant_genetics_and_genomics/10.3389/fpls.2011.00092/abstract
N2  - In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis.
ER  -

Základní údaje
Originální název	Dynamic network-based epistasis analysis: Boolean examples
Autoři	AZPEITIA, Eugenio (484 Mexiko), Mariana BENITEZ (484 Mexiko, domácí), Pablo PADILLA-LONGORIA (484 Mexiko), Carlos ESPINOSA-SOTO (484 Mexiko) a Elena R. ALVAREZ-BUYLLA (484 Mexiko, garant).
Vydání	Frontiers in Plant Science, Switzerland, Frontiers, 2011, 1664-462X.

Další údaje
Originální jazyk	angličtina
Typ výsledku	Článek v odborném periodiku
Obor	Genetika a molekulární biologie
Stát vydavatele	Švýcarsko
Utajení	není předmětem státního či obchodního tajemství
WWW	Article freely available
Kód RIV	RIV/00216224:14740/11:00055437
Organizační jednotka	Středoevropský technologický institut
Doi	http://dx.doi.org/10.3389/fpls.2011.00092
UT WoS	000208837500092
Klíčová slova anglicky	Boolean network; dynamic model; epistasis
Štítky	ok, rivok
Příznaky	Mezinárodní význam
Změnil	Změnila: Olga Křížová, učo 56639. Změněno: 26. 3. 2012 22:56.

Anotace
In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis.

Anotace

In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis.

Návaznosti
LC06034, projekt VaV	Název: Regulace morfogeneze rostlinných buněk a orgánů
LC06034, projekt VaV	Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Regulace morfogeneze rostlinných buněk a orgánů