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Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function

author

Alisdair R Fernie

Takayuki Tohge

published in: Nature Protocols

date of publication: 2010-06-10

main subject: metabolomics, informatics, genetic diversity

Cites articles 149

Date

Title

Authors

2010-02-26

Combined transcript and metabolite profiling of Arabidopsis grown under widely variant growth conditions facilitates the identification of novel metabolite-mediated regulation of gene expression

Matthew A Hannah, Dirk Steinhauser, Lothar Willmitzer, Alisdair R Fernie
2009-03-01

Drought stress increases the production of 5-hydroxynorvaline in two C4 grasses

Elizabete Carmo-Silva, Martin Parry
2009-08-01

A metabolic signature of the beneficial interaction of the endophyte paenibacillus sp. isolate and in vitro-grown poplar plants revealed by metabolomics.

Wolfram Weckwerth
2009-08-10

Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance

Ed Newbigin, Ute Roessner, Mark Tester, Tony Bacic
2009-04-09

Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination

Atsushi Fukushima, Miyako Kusano, Hitoshi Sakakibara, Kazuki Saito
2009-03-13

A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis.

Hiroyuki Ohta, Kazuki Saito, Mie Shimojima, Masami Yokota Hirai, Keiichi Mochida, Yuji Sawada, Fumio Matsuda, Yozo Okazaki, Kiminori Toyooka, Tomoko Narisawa, Akiko Hirai
2009-08-25

Functional genomics for plant natural product biosynthesis

Kazuki Saito, Keiko Yonekura-Sakakibara
2009-08-01

13C isotope-labeled metabolomes allowing for improved compound annotation and relative quantification in liquid chromatography-mass spectrometry-based metabolomic research

Karin Köhl
2009-03-13

Web-based resources for mass-spectrometry-based metabolomics: a user's guide

Alisdair R Fernie, Takayuki Tohge
2009-02-01

MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites

Kazuki Saito, Kazuo Shinozaki, Keiko Yonekura-Sakakibara, Takashi Kuromori
2009-01-14

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

Catherine Deborde, Johann Petit, Martine Lemaire-Chamley, Christophe Rothan, Annick Moing, Michael Maucourt, Stéphane Bernillon, Fabien Mounet, Virginie Garcia, Jean-Luc Giraudel
2009-08-26

Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism

Miyako Kusano, Masaki Mori, Hitoshi Sakakibara, Kazuki Saito
2009-04-02

The LAP1 MYB transcription factor orchestrates anthocyanidin biosynthesis and glycosylation in Medicago

Luzia V. Modolo
2009-09-09

The grapevine R2R3-MYB transcription factor VvMYBF1 regulates flavonol synthesis in developing grape berries

Bernd Weisshaar, Ralf Stracke, Amanda R Walker, Simon P Robinson
2009-01-02

MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis
2009-08-12

Plastidial glyceraldehyde-3-phosphate dehydrogenase deficiency leads to altered root development and affects the sugar and amino acid balance in Arabidopsis

Jesús Muñoz-Bertomeu, José Miguel Mulet Salort, Javier Pozueta-Romero, Juan Segura, Roc Ros, Edurne Baroja Fernández
2009-11-06

Molecular identification and functional characterization of Arabidopsis thaliana mitochondrial and chloroplastic NAD+ carrier proteins

Adriano Nunes Nesi, Alisdair R Fernie
2009-04-24

Application of GC-MS for the detection of lipophilic compounds in diverse plant tissues

Alisdair R Fernie
2009-06-15

A plant thiolase involved in benzoic acid biosynthesis and volatile benzenoid production

Alex Van Moerkercke, Robert C Schuurink, Eran Pichersky
2009-08-27

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Dirk Steinhauser, George W. Bassel, Staffan Persson, Björn Usadel, Federico Manuel Giorgi, Amanda Froehlich Chow, Nicholas J Provart
2009-04-28

Web-queryable large-scale data sets for hypothesis generation in plant biology

Siobhan M Brady, Nicholas J Provart
2009-05-01

Metabolomics-oriented isolation and structure elucidation of 37 compounds including two anthocyanins from Arabidopsis thaliana.

Miyako Kusano, Kazuki Saito, Ryo Nakabayashi, Mami Yamazaki, Takayuki Tohge, Keiko Yonekura-Sakakibara, Hiromitsu Takayama, Mariko Kitajima, Noriyuki Kogure
2009-07-15

RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice

Gynheung An, Ju-Kon Kim
2009-10-01

Network visualization and analysis of gene expression data using BioLayout Express(3D).

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2009-09

Identification of heterotic metabolite QTL inArabidopsis thalianaRIL and IL populations

Jan Lisec, Albrecht E. Melchinger, Rhonda C Meyer, Lothar Willmitzer, Joachim Selbig
2008-11-25

Adjustment of growth and central metabolism to a mild but sustained nitrogen-limitation in Arabidopsis.

Adriano Nunes Nesi, Alisdair R Fernie, Mark Stitt, Marek Szecówka
2008-08-29

Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis.

Kazuki Saito, Takayuki Tohge, Keiko Yonekura-Sakakibara
2008-05-29

Differential gene expression profiles of red and green forms of Perilla frutescens leading to comprehensive identification of anthocyanin biosynthetic genes.

Kazuki Saito, Mami Yamazaki
2008-05-30

Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome

Barbara Ann Halkier, Daniel J. Kliebenstein
2008-05-01

Screening for wound-induced oxylipins in Arabidopsis thaliana by differential HPLC-APCI/MS profiling of crude leaf extracts and subsequent characterisation by capillary-scale NMR.

Jean-Luc Wolfender, Edward E Farmer
2008-12-15

High-Resolution Direct Infusion-Based Mass Spectrometry in Combination with Whole13C Metabolome Isotope Labeling Allows Unambiguous Assignment of Chemical Sum Formulas

Jan Lisec, Lothar Willmitzer
2008-02-07

Metabolite annotations based on the integration of mass spectral information

Article - wd:Q84387320

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