The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over‐expressing an MYB transcription factor
Abstract
Summary: The integration of metabolomics and transcriptomics can provide precise information on gene‐to‐metabolite networks for identifying the function of unknown genes unless there has been a post‐transcriptional modification. Here, we report a comprehensive analysis of the metabolome and transcriptome of Arabidopsis thaliana over‐expressing the PAP1 gene encoding an MYB transcription factor, for the identification of novel gene functions involved in flavonoid biosynthesis. For metabolome analysis, we performed flavonoid‐targeted analysis by high‐performance liquid chromatography‐mass spectrometry and non‐targeted analysis by Fourier‐transform ion‐cyclotron mass spectrometry with an ultrahigh‐resolution capacity. This combined analysis revealed the specific accumulation of cyanidin and quercetin derivatives, and identified eight novel anthocyanins from an array of putative 1800 metabolites in PAP1 over‐expressing plants. The transcriptome analysis of 22 810 genes on a DNA microarray revealed the induction of 38 genes by ectopic PAP1 over‐expression. In addition to well‐known genes involved in anthocyanin production, several genes with unidentified functions or annotated with putative functions, encoding putative glycosyltransferase, acyltransferase, glutathione S ‐transferase, sugar transporters and transcription factors, were induced by PAP1 . Two putative glycosyltransferase genes ( At5g17050 and At4g14090 ) induced by PAP1 expression were confirmed to encode flavonoid 3‐ O ‐glucosyltransferase and anthocyanin 5‐ O ‐glucosyltransferase, respectively, from the enzymatic activity of their recombinant proteins in vitro and results of the analysis of anthocyanins in the respective T‐DNA‐inserted mutants. The functional genomics approach through the integration of metabolomics and transcriptomics presented here provides an innovative means of identifying novel gene functions involved in plant metabolism.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
Cited by
The Phenylpropanoid Pathway in Arabidopsis
Fraser, C. M., & Chapple, C. (2011) · The Arabidopsis Book · doi:10.1199/tab.0152 · Cited by 860
Lin-Wang, K., Bolitho, K., Grafton, K., Kortstee, A., Karunairetnam, S., McGhie, T. K., Espley, R. V., Hellens, R. P., & Allan, A. C. (2010) · BMC Plant Biology · doi:10.1186/1471-2229-10-50 · Cited by 699
Wu, A., Allu, A. D., Garapati, P., Siddiqui, H., Dortay, H., Zanor, M.-I., Asensi-Fabado, M. A., Munné-Bosch, S., Antonio, C., Tohge, T., et al. (2012) · The Plant Cell · doi:10.1105/tpc.111.090894 · Cited by 601
Self-citationLi, P., Li, Y., Zhang, F., Zhang, G., Jiang, X., Yu, H., & Hou, B. (2017) · The Plant Journal · doi:10.1111/tpj.13324 · Cited by 574
Metabolomics-assisted breeding: a viable option for crop improvement?
Fernie, A. R., & Schauer, N. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.10.010 · Cited by 550
Metadata
- Authors
- Tohge, T., Nishiyama, Y., Hirai, M. Y., Yano, M., Nakajima, J., Awazuhara, M., Inoue, E., Takahashi, H., Goodenowe, D. B., Kitayama, M., Noji, M., Yamazaki, M., & Saito, K.
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2005-03-07
- Volume
- 42
- Issue
- 2
- Pages
- 218-235
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- OpenAlex
- W2115831900
- Cited by
- 985
- References
- 1
- FWCI
- 21.09
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over‐expressing an MYB transcription factor. https://app.cochat.ai/papers/10.1111/j.1365-313x.2005.02371.x
- The paper
- Tohge, T., Nishiyama, Y., Hirai, M. Y., Yano, M., Nakajima, J., Awazuhara, M., Inoue, E., Takahashi, H., Goodenowe, D. B., Kitayama, M., Noji, M., Yamazaki, M., & Saito, K. (2005). Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over‐expressing an MYB transcription factor. The Plant Journal. https://doi.org/10.1111/j.1365-313x.2005.02371.x
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
