(Q33577402)

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Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis

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scholarly article

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Europe PubMed Central

PubMed publication ID

28 July 2017

Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis (English)

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

2

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Annick Moing

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Europe PubMed Central

PubMed publication ID

28 July 2017

author name string

Elizabeth Allen

1

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Timothy Md Ebbels

3

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Mickaël Maucourt

4

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

A Deri Tomos

5

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Dominique Rolin

6

1 reference

Europe PubMed Central

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28 July 2017

Mark A Hooks

7

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

publication date

13 May 2010

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Europe PubMed Central

PubMed publication ID

28 July 2017

BMC Systems Biology

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Europe PubMed Central

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28 July 2017

4

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

62

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis

1 reference

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28 July 2018

1H NMR, GC-EI-TOFMS, and data set correlation for fruit metabolomics: application to spatial metabolite analysis in melon

1 reference

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28 July 2018

Plant hormones and nutrient signaling.

1 reference

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28 July 2018

An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

1 reference

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28 July 2018

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1

1 reference

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28 July 2018

Plant systems biology comes of age.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Metabolomics integrated with transcriptomics: assessing systems response to sulfur-deficiency stress

1 reference

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28 July 2018

Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'.

1 reference

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28 July 2018

Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages

1 reference

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28 July 2018

PIL5, a phytochrome-interacting bHLH protein, regulates gibberellin responsiveness by binding directly to the GAI and RGA promoters in Arabidopsis seeds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis

1 reference

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28 July 2018

Genome-wide analysis of the Arabidopsis leaf transcriptome reveals interaction of phosphate and sugar metabolism

1 reference

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28 July 2018

Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Seed dormancy and the control of germination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Sugar sensing and signaling in plants: conserved and novel mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Metabolic regulation underlying tomato fruit development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Regulation of metabolic networks: understanding metabolic complexity in the systems biology era.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Characterization of Arabidopsis fluoroacetate-resistant mutants reveals the principal mechanism of acetate activation for entry into the glyoxylate cycle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Lactate in solid malignant tumors: potential basis of a metabolic classification in clinical oncology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Heard it through the grapevine? ABA and sugar cross-talk: the ASR story

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Parallel analysis of transcript and metabolic profiles: a new approach in systems biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments

1 reference

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28 July 2018

Co-ordinate regulation of genes involved in storage lipid mobilization in Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Carbon and nitrogen sensing and signaling in plants: emerging 'matrix effects'.

1 reference

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28 July 2018

Integrated studies on plant biology using multiparallel techniques

1 reference

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28 July 2018

ocs element promoter sequences are activated by auxin and salicylic acid in Arabidopsis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Metabolic repression of transcription in higher plants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

28 July 2018

Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

CHOTTO1, a double AP2 domain protein of Arabidopsis thaliana, regulates germination and seedling growth under excess supply of glucose and nitrate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Elucidating the germination transcriptional program using small molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Components of Arabidopsis defense- and ethylene-signaling pathways regulate susceptibility to Cauliflower mosaic virus by restricting long-distance movement

1 reference

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31 October 2018

Gene expression profiling reveals defined functions of the ATP-binding cassette transporter COMATOSE late in phase II of germination.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Arabidopsis seed development and germination is associated with temporally distinct metabolic switches.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Plant metabolomics: towards biological function and mechanism

1 reference

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31 October 2018

Arabidopsis ABA INSENSITIVE4 regulates lipid mobilization in the embryo and reveals repression of seed germination by the endosperm.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Identification of sugar-modulated genes and evidence for in vivo sugar sensing in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

A genome-wide analysis of the effects of sucrose on gene expression in Arabidopsis seedlings under anoxia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Sugar sensing and signalling networks in plants.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Reserve mobilization in the Arabidopsis endosperm fuels hypocotyl elongation in the dark, is independent of abscisic acid, and requires PHOSPHOENOLPYRUVATE CARBOXYKINASE1.

1 reference

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31 October 2018

The potassium-dependent transcriptome of Arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling

1 reference

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31 October 2018

Lactate: mirror and motor of tumor malignancy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

SUGAR-INDUCED SIGNAL TRANSDUCTION IN PLANTS.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Acetate non-utilizing mutants of Arabidopsis: evidence that organic acids influence carbohydrate perception in germinating seedlings

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Gibberellin biosynthesis and response during Arabidopsis seed germination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Sugar and hormone connections

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

The ABSCISIC ACID INSENSITIVE 3 (ABI3) gene is modulated by farnesylation and is involved in auxin signaling and lateral root development in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2890501

31 October 2018

Arabidopsis A BOUT DE SOUFFLE, which is homologous with mammalian carnitine acyl carrier, is required for postembryonic growth in the light.

1 reference

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31 October 2018

Germination and storage reserve mobilization are regulated independently in Arabidopsis

1 reference

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31 October 2018

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1 reference

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31 October 2018

The auxin, hydrogen peroxide and salicylic acid induced expression of the Arabidopsis GST6 promoter is mediated in part by an ocs element

1 reference

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31 October 2018

Cold and Light Control Seed Germination through the bHLH Transcription Factor SPATULA

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31 October 2018

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31 October 2018

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1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

12 December 2020

based on heuristic

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1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Seed Germination and Dormancy

1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

12 December 2020

based on heuristic

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Concentration Measurement by Proton NMR Using the ERETIC Method

1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

12 December 2020

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Lactate adversely affects the in vitro formation of endothelial cell tubular structures through the action of TGF-beta1

1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

12 December 2020

based on heuristic

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PICKLE is required for SOLITARY-ROOT/IAA14-mediated repression of ARF7 and ARF19 activity during Arabidopsis lateral root initiation

1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

12 December 2020

based on heuristic

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On the processing of metabolic information through metabolite-gene communication networks: an approach for modelling causality

1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Gene expression profiles of Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism

1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

12 December 2020

based on heuristic

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1 reference

https://pubmed.ncbi.nlm.nih.gov/20465807

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based on heuristic

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Identifiers

10.1186/1752-0509-4-62

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

DBLP publication ID

journals/bmcsb/AllenMEMTRH10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

ResearchGate publication ID

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