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Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress

Vanessa Vermeirssen, Inge De Clercq UGent, Thomas Van Parys UGent, Frank Van Breusegem UGent and Yves Van de Peer UGent (2014) PLANT CELL. 26(12). p.4656-4679
abstract
The abiotic stress response in plants is complex and tightly controlled by gene regulation. We present an abiotic stress gene regulatory network of 200,014 interactions for 11,938 target genes by integrating four complementary reverse-engineering solutions through average rank aggregation on an Arabidopsis thaliana microarray expression compendium. This ensemble performed the most robustly in benchmarking and greatly expands upon the availability of interactions currently reported. Besides recovering 1182 known regulatory interactions, cis-regulatory motifs and coherent functionalities of target genes corresponded with the predicted transcription factors. We provide a valuable resource of 572 abiotic stress modules of coregulated genes with functional and regulatory information, from which we deduced functional relationships for 1966 uncharacterized genes and many regulators. Using gain-and loss-of-function mutants of seven transcription factors grown under control and salt stress conditions, we experimentally validated 141 out of 271 predictions (52% precision) for 102 selected genes and mapped 148 additional transcription factor-gene regulatory interactions (49% recall). We identified an intricate core oxidative stress regulatory network where NAC13, NAC053, ERF6, WRKY6, and NAC032 transcription factors interconnect and function in detoxification. Our work shows that ensemble reverse-engineering can generate robust biological hypotheses of gene regulation in a multicellular eukaryote that can be tested by medium-throughput experimental validation.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
SALICYLIC-ACID, DIFFERENTIAL EXPRESSION ANALYSIS, ABIOTIC STRESS, SYSTEMS BIOLOGY, AMINO-ACID-METABOLISM, ENCODING MITOCHONDRIAL, RESPONSIVE TRANSCRIPTION, COEXPRESSION ANALYSIS, RETROGRADE REGULATION, PROTEIN RESPONSE
journal title
PLANT CELL
Plant Cell
volume
26
issue
12
pages
4656 - 4679
Web of Science type
Article
Web of Science id
000348646000012
JCR category
PLANT SCIENCES
JCR impact factor
9.338 (2014)
JCR rank
4/204 (2014)
JCR quartile
1 (2014)
ISSN
1040-4651
DOI
10.1105/tpc.114.131417
project
Bioinformatics: from nucleotids to networks (N2N)
project
Biotechnology for a sustainable economy (Bio-Economy)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
5853084
handle
http://hdl.handle.net/1854/LU-5853084
date created
2015-02-19 09:50:07
date last changed
2016-12-19 15:46:43
@article{5853084,
  abstract     = {The abiotic stress response in plants is complex and tightly controlled by gene regulation. We present an abiotic stress gene regulatory network of 200,014 interactions for 11,938 target genes by integrating four complementary reverse-engineering solutions through average rank aggregation on an Arabidopsis thaliana microarray expression compendium. This ensemble performed the most robustly in benchmarking and greatly expands upon the availability of interactions currently reported. Besides recovering 1182 known regulatory interactions, cis-regulatory motifs and coherent functionalities of target genes corresponded with the predicted transcription factors. We provide a valuable resource of 572 abiotic stress modules of coregulated genes with functional and regulatory information, from which we deduced functional relationships for 1966 uncharacterized genes and many regulators. Using gain-and loss-of-function mutants of seven transcription factors grown under control and salt stress conditions, we experimentally validated 141 out of 271 predictions (52\% precision) for 102 selected genes and mapped 148 additional transcription factor-gene regulatory interactions (49\% recall). We identified an intricate core oxidative stress regulatory network where NAC13, NAC053, ERF6, WRKY6, and NAC032 transcription factors interconnect and function in detoxification. Our work shows that ensemble reverse-engineering can generate robust biological hypotheses of gene regulation in a multicellular eukaryote that can be tested by medium-throughput experimental validation.},
  author       = {Vermeirssen, Vanessa and De Clercq, Inge and Van Parys, Thomas and Van Breusegem, Frank and Van de Peer, Yves},
  issn         = {1040-4651},
  journal      = {PLANT CELL},
  keyword      = {SALICYLIC-ACID,DIFFERENTIAL EXPRESSION ANALYSIS,ABIOTIC STRESS,SYSTEMS BIOLOGY,AMINO-ACID-METABOLISM,ENCODING MITOCHONDRIAL,RESPONSIVE TRANSCRIPTION,COEXPRESSION ANALYSIS,RETROGRADE REGULATION,PROTEIN RESPONSE},
  language     = {eng},
  number       = {12},
  pages        = {4656--4679},
  title        = {Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress},
  url          = {http://dx.doi.org/10.1105/tpc.114.131417},
  volume       = {26},
  year         = {2014},
}

Chicago
Vermeirssen, Vanessa, Inge De Clercq, Thomas Van Parys, Frank Van Breusegem, and Yves Van de Peer. 2014. “Arabidopsis Ensemble Reverse-engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress.” Plant Cell 26 (12): 4656–4679.
APA
Vermeirssen, Vanessa, De Clercq, I., Van Parys, T., Van Breusegem, F., & Van de Peer, Y. (2014). Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress. PLANT CELL, 26(12), 4656–4679.
Vancouver
1.
Vermeirssen V, De Clercq I, Van Parys T, Van Breusegem F, Van de Peer Y. Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress. PLANT CELL. 2014;26(12):4656–79.
MLA
Vermeirssen, Vanessa, Inge De Clercq, Thomas Van Parys, et al. “Arabidopsis Ensemble Reverse-engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress.” PLANT CELL 26.12 (2014): 4656–4679. Print.