Identification of gene interactions in fungal-plant symbiosis through discrete dynamical system modelling

J. G C Angeles, Z. Ouyang, A. M. Aguirre, Peter Lammers, M. Song

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Fungal-plant root associations involve nutrient exchanges, between the partners and the soil, particularly phosphate, that benefit both organisms. Discrete dynamical system (DDS) models are reconstructed to capture gene regulation in the arbuscular mycorrhizae Glomus versiforme-Medicago trunculata root symbiosis. Previously published time-course gene expression data derived from various days post-inoculation were clustered to identify genes co-regulated in mycorrhizal roots. Uncolonised roots grown with high phosphate provide a key nutritional control condition. First-order linear DDS models were created using a data-driven method to fit to the observed gene expression data. The result of the modelling constitutes active gene interactions in the regulatory network of the plant root at 8, 15, 22, 31 and 36 days post-inoculation. These genes are involved in basic metabolism, development, oxidative stress and defense pathways, and show consistent dynamic behaviours in the model. The functions of previously unannotated genes were further elucidated from the developed system maps.

Original languageEnglish (US)
Pages (from-to)414-428
Number of pages15
JournalIET Systems Biology
Volume3
Issue number5
DOIs
StatePublished - 2009
Externally publishedYes

Fingerprint

Symbiosis
Discrete Dynamical Systems
System Modeling
Dynamical systems
Genes
Gene expression
Roots
Gene
Interaction
Plant Roots
Gene Expression Data
Phosphates
Phosphate
Oxidative stress
Oxidative Stress
Mycorrhizae
Gene Expression
Medicago
Linear Dynamical Systems
Metabolism

ASJC Scopus subject areas

  • Biotechnology
  • Cell Biology
  • Genetics
  • Molecular Biology
  • Modeling and Simulation

Cite this

Identification of gene interactions in fungal-plant symbiosis through discrete dynamical system modelling. / Angeles, J. G C; Ouyang, Z.; Aguirre, A. M.; Lammers, Peter; Song, M.

In: IET Systems Biology, Vol. 3, No. 5, 2009, p. 414-428.

Research output: Contribution to journalArticle

Angeles, J. G C ; Ouyang, Z. ; Aguirre, A. M. ; Lammers, Peter ; Song, M. / Identification of gene interactions in fungal-plant symbiosis through discrete dynamical system modelling. In: IET Systems Biology. 2009 ; Vol. 3, No. 5. pp. 414-428.
@article{0b600b69fb45472e96f4030ea4247f23,
title = "Identification of gene interactions in fungal-plant symbiosis through discrete dynamical system modelling",
abstract = "Fungal-plant root associations involve nutrient exchanges, between the partners and the soil, particularly phosphate, that benefit both organisms. Discrete dynamical system (DDS) models are reconstructed to capture gene regulation in the arbuscular mycorrhizae Glomus versiforme-Medicago trunculata root symbiosis. Previously published time-course gene expression data derived from various days post-inoculation were clustered to identify genes co-regulated in mycorrhizal roots. Uncolonised roots grown with high phosphate provide a key nutritional control condition. First-order linear DDS models were created using a data-driven method to fit to the observed gene expression data. The result of the modelling constitutes active gene interactions in the regulatory network of the plant root at 8, 15, 22, 31 and 36 days post-inoculation. These genes are involved in basic metabolism, development, oxidative stress and defense pathways, and show consistent dynamic behaviours in the model. The functions of previously unannotated genes were further elucidated from the developed system maps.",
author = "Angeles, {J. G C} and Z. Ouyang and Aguirre, {A. M.} and Peter Lammers and M. Song",
year = "2009",
doi = "10.1049/iet-syb.2008.0164",
language = "English (US)",
volume = "3",
pages = "414--428",
journal = "IET Systems Biology",
issn = "1751-8849",
publisher = "Institution of Engineering and Technology",
number = "5",

}

TY - JOUR

T1 - Identification of gene interactions in fungal-plant symbiosis through discrete dynamical system modelling

AU - Angeles, J. G C

AU - Ouyang, Z.

AU - Aguirre, A. M.

AU - Lammers, Peter

AU - Song, M.

PY - 2009

Y1 - 2009

N2 - Fungal-plant root associations involve nutrient exchanges, between the partners and the soil, particularly phosphate, that benefit both organisms. Discrete dynamical system (DDS) models are reconstructed to capture gene regulation in the arbuscular mycorrhizae Glomus versiforme-Medicago trunculata root symbiosis. Previously published time-course gene expression data derived from various days post-inoculation were clustered to identify genes co-regulated in mycorrhizal roots. Uncolonised roots grown with high phosphate provide a key nutritional control condition. First-order linear DDS models were created using a data-driven method to fit to the observed gene expression data. The result of the modelling constitutes active gene interactions in the regulatory network of the plant root at 8, 15, 22, 31 and 36 days post-inoculation. These genes are involved in basic metabolism, development, oxidative stress and defense pathways, and show consistent dynamic behaviours in the model. The functions of previously unannotated genes were further elucidated from the developed system maps.

AB - Fungal-plant root associations involve nutrient exchanges, between the partners and the soil, particularly phosphate, that benefit both organisms. Discrete dynamical system (DDS) models are reconstructed to capture gene regulation in the arbuscular mycorrhizae Glomus versiforme-Medicago trunculata root symbiosis. Previously published time-course gene expression data derived from various days post-inoculation were clustered to identify genes co-regulated in mycorrhizal roots. Uncolonised roots grown with high phosphate provide a key nutritional control condition. First-order linear DDS models were created using a data-driven method to fit to the observed gene expression data. The result of the modelling constitutes active gene interactions in the regulatory network of the plant root at 8, 15, 22, 31 and 36 days post-inoculation. These genes are involved in basic metabolism, development, oxidative stress and defense pathways, and show consistent dynamic behaviours in the model. The functions of previously unannotated genes were further elucidated from the developed system maps.

UR - http://www.scopus.com/inward/record.url?scp=70349559072&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70349559072&partnerID=8YFLogxK

U2 - 10.1049/iet-syb.2008.0164

DO - 10.1049/iet-syb.2008.0164

M3 - Article

C2 - 21028931

AN - SCOPUS:70349559072

VL - 3

SP - 414

EP - 428

JO - IET Systems Biology

JF - IET Systems Biology

SN - 1751-8849

IS - 5

ER -