OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants

OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants. Srivastava, V., Obudulu, O., Bygdell, J., Löfstedt, T., Rydén, P., Nilsson, R., Ahnlund, M., Johansson, A., Jonsson, P., Freyhult, E., Qvarnström, J., Karlsson, J., Melzer, M., Moritz, T., Trygg, J., Hvidsten, T. R., & Wingsle, G. BMC Genomics, 14(1):893, December, 2013.

Paper doi abstract bibtex

Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.

@article{srivastava_onpls_2013,
	title = {{OnPLS} integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic {hipI}- superoxide dismutase {Populus} plants},
	volume = {14},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/1471-2164-14-893},
	doi = {10/f2zk6q},
	abstract = {Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Srivastava, Vaibhav and Obudulu, Ogonna and Bygdell, Joakim and Löfstedt, Tommy and Rydén, Patrik and Nilsson, Robert and Ahnlund, Maria and Johansson, Annika and Jonsson, Pär and Freyhult, Eva and Qvarnström, Johanna and Karlsson, Jan and Melzer, Michael and Moritz, Thomas and Trygg, Johan and Hvidsten, Torgeir R. and Wingsle, Gunnar},
	month = dec,
	year = {2013},
	keywords = {OnPLS, Oxidative stress, Poplar, Statistical integration, Systems biology},
	pages = {893},
}

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