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

By M. Hirai, Mitsuru Yano, D. Goodenowe, Shigehiko Kanaya, Tomoko Kimura, M. Awazuhara, Masanori Arita, T. Fujiwara, Kazuki Saito. Proceedings of the National Academy of Sciences of the United States of America, 2004

764 citations recorded by the source corpus.

Subfields: Biochemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/eec099a0b1f0630a1563193c9cf03157727ede27

Citations in the corpus

• Potential of metabolomics as a functional genomics tool. (2004, neutral): “As the comprehensiveness increases and bioinformatic tools mature, functional metabolomic information can be linked to transcriptome and proteome datasets to enable a better understanding of plant biology [41, 42 ].”
• The model organism as a system: integrating 'omics' data sets (2006, neutral): “, as well as to analyse the nutrient-starvation stress response in Arabidopsis thaliana”
• Metabolomics for functional genomics, systems biology, and biotechnology. (2010, neutral): “The effects of nitrogen starvation and readdition on gene expression and cellular metabolism were suggested by omics analysis in a similar way (79, 83, 171).”
• Effects of nitrogen deficiency on leaf photosynthesis, carbohydrate status and biomass production in two olive cultivars 'Meski' and 'Koroneiki' (2010, neutral): “N deficiency results in accumulation of carbohydrates (sugars and starch) in the leaves, higher levels of carbon allocated to the roots and an increase in root-toshoot biomass ratio (Hirai et al., 2004; Scheible et al., 2004; Remans et al., 2006).”
• Mass spectrometry-based metabolomics. (2007, neutral): “…both extracts using four different ionization modes, and a single empirical formula could be assigned to over half of them with an error of 1 ppm. Hirai et al. (2004) used FT-ICRMS for metabolic fingerprinting of Arabidopsis thaliana extracts in an integrated transcriptomics and metabolomics…”
• The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. (2007, neutral): “…effects on global gene expression in Arabidopsis and other plant species by several research groups (Brown et al., 2005; Chen et al., 2002; Desikan et al., 2001; Fowler and Thomashow, 2002; Hirai et al., 2004; Kreps et al., 2002; Rossel et al., 2002; Seki et al., 2001, 2002; Ulm et al., 2004).”
• Approaches for extracting practical information from gene co-expression networks in plant biology. (2007, neutral): “Consequently, the authors found regulatory linkage among nutrient deficiency, primary metabolism and glucosinolate metabolism (Hirai et al. 2004).”
• The use of metabolomics to dissect plant responses to abiotic stresses (2012, neutral): “[111] revealed gene to metabolite regulatory networks of glucosinolate synthesis and primary metabolism under sulphur- and nitrogen-limited conditions by applying Table 1 Number of metabolites that changed their abundance under each stress condition”
• Linking aboveground and belowground interactions via induced plant defenses. (2005, neutral): “one species [70], diseased and healthy plants [71], and plants under different nutrient regimes [ 72 ].”
• Gene function beyond the single trait: natural variation, gene effects, and evolutionary ecology in Arabidopsis thaliana (2005, neutral): “The prediction of the extent and nature of pleiotropic effects for any particular gene remains poor, partly due to a lack of knowledge of the organization of gene networks in the organism (but see Hirai et al .”