Evidence map›Paper›PMID 25533953›Full record

ArticleNature2015

An Arabidopsis gene regulatory network for secondary cell wall synthesis.

M Taylor-Teeples, L Lin, M de Lucas, G Turco, T W Toal, A Gaudinier, N F Young, G M Trabucco, M T Veling, R Lamothe and 17 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 374 papers.

0numbers the graph read from it
0cells of the map it votes in
374citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

374 citing papers in PubMed.

  1. Review
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  19. Review
  20. The role of theFrontiers in plant science · 2026
    Article

314 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

27 authors.

M Taylor-Teeples1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
L LinBiology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
M de Lucas1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
G Turco1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
T W Toal1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
A Gaudinier1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
N F YoungBiology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
G M TrabuccoBiology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
M T VelingBiology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
R LamotheBiology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
P P HandakumburaBiology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
G XiongDepartment of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.
C WangDepartment of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
J CorwinDepartment of Plant Sciences, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
A Tsoukalas1] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Department of Computer Science, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
L ZhangCold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
D Ware1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] US Department of Agriculture, Agricultural Research Service, Ithaca, New York 14853, USA.
M PaulyDepartment of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.
D J KliebensteinDepartment of Plant Sciences, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
K DeheshDepartment of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
I Tagkopoulos1] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Department of Computer Science, University of California Davis, One Shields Avenue, Davis, California 95616, USA.
G BretonSection of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.
J L Pruneda-PazSection of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.
S E AhnertTheory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
S A KaySection of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.
S P HazenBiology Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.
S M Brady1] Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, California 95616, USA [2] Genome Center, University of California Davis, One Shields Avenue, Davis, California 95616, USA.

Funding

UC Davis Biology ProgramR25GM056765 · NIGMS · UNIVERSITY OF CALIFORNIA DAVIS · PI GOMES, ALDRIN V. · 1998 to 2019
$9.7M
GENETIC ANALYSIS OF CIRCADIAN RHYTHMS IN ARABIDOPSISR01GM056006 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI KAY, STEVE A, PRUNEDA-PAZ, JOSE L · 1996 to 2016
$6.0M
Defining the Retrograde Plastid-to-Nucleus Stress Signaling PathwayR01GM107311 · NIGMS · UNIVERSITY OF CALIFORNIA RIVERSIDE · PI DEHESH, KATAYOON · 2013 to 2021
$2.5M
The Arabidopsis Transcription Factor ORFeome and downstream genomic applicationRC2GM092412 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ECKER, JOSEPH R, KAY, STEVE A · 2009 to 2010
$2.0M
NIGMS NIH HHS R01 GM056006NIGMS NIH HHS R01GM056006NIGMS NIH HHS R01 GM107311NIGMS NIH HHS R01GM107311NIGMS NIH HHS R25 GM056765NIGMS NIH HHS RC2 GM092412NIGMS NIH HHS RC2GM092412
6 · The paper itself

Abstract

The plant cell wall is an important factor for determining cell shape, function and response to the environment. Secondary cell walls, such as those found in xylem, are composed of cellulose, hemicelluloses and lignin and account for the bulk of plant biomass. The coordination between transcriptional regulation of synthesis for each polymer is complex and vital to cell function. A regulatory hierarchy of developmental switches has been proposed, although the full complement of regulators remains unknown. Here we present a protein-DNA network between Arabidopsis thaliana transcription factors and secondary cell wall metabolic genes with gene expression regulated by a series of feed-forward loops. This model allowed us to develop and validate new hypotheses about secondary wall gene regulation under abiotic stress. Distinct stresses are able to perturb targeted genes to potentially promote functional adaptation. These interactions will serve as a foundation for understanding the regulation of a complex, integral plant component.

Indexed as

ArabidopsisArabidopsis ProteinsCell WallDNA, PlantE2F Transcription FactorsFeedbackGene Expression Regulation, DevelopmentalGene Expression Regulation, PlantGene Regulatory NetworksIron DeficienciesOrgan SpecificityPromoter Regions, GeneticReproducibility of ResultsSalinityTime FactorsTranscription FactorsArabidopsis ProteinsDNA, PlantE2FC protein, ArabidopsisE2F Transcription FactorsTranscription FactorsVND7 protein, Arabidopsis

Identifiers

PMID25533953
PMCPMC4333722

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.