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Grene R, Klumas C, Suren H, et al. Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). Front Plant Sci. 2012;3:241doi: 10.3389/fpls.2012.00241.
Grene, R., Klumas, C., Suren, H., Yang, K., Collakova, E., Myers, E., Heath, L. S., & Holliday, J. A. (2012). Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). Frontiers in plant science, 3241. https://doi.org/10.3389/fpls.2012.00241
Grene, Ruth, et al. "Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis)." Frontiers in plant science vol. 3 (2012): 241. doi: https://doi.org/10.3389/fpls.2012.00241
Grene R, Klumas C, Suren H, Yang K, Collakova E, Myers E, Heath LS, Holliday JA. Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). Front Plant Sci. 2012 Oct 29;3:241. doi: 10.3389/fpls.2012.00241. eCollection 2012. PMID: 23112803; PMCID: PMC3482696.
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Front Plant Sci. 2012 Oct 29;3:241. doi: 10.3389/fpls.2012.00241. eCollection 2012.

Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis).

Frontiers in plant science

Ruth Grene, Curtis Klumas, Haktan Suren, Kuan Yang, Eva Collakova, Elijah Myers, Lenwood S Heath, Jason A Holliday

Affiliations

  1. Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech Blacksburg, VA, USA.

PMID: 23112803 PMCID: PMC3482696 DOI: 10.3389/fpls.2012.00241

Abstract

Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported a microarray study of the freezing acclimation period in Sitka spruce (Picea sitchensis) in which a large number of candidate genes for climatic adaptation were identified. In the current paper, we apply additional systems biology tools to these data to further probe changes in the levels of genes and metabolites and activities of associated pathways that regulate this complex developmental transition. One aspect of this adaptive process that is not well understood is the role of the cell wall. Our data suggest coordinated metabolic and signaling responses leading to cell wall remodeling. Co-expression of genes encoding proteins associated with biosynthesis of structural and non-structural cell wall carbohydrates was observed, which may be regulated by ethylene signaling components. At the same time, numerous genes, whose products are putatively localized to the endomembrane system and involved in both the synthesis and trafficking of cell wall carbohydrates, were up-regulated. Taken together, these results suggest a link between ethylene signaling and biosynthesis, and targeting of cell wall related gene products during the period of winter hardening. Automated Layout Pipeline for Inferred NEtworks (ALPINE), an in-house plugin for the Cytoscape visualization environment that utilizes the existing GeneMANIA and Mosaic plugins, together with the use of visualization tools, provided images of proposed signaling processes that became active over the time course of winter hardening, particularly at later time points in the process. The resulting visualizations have the potential to reveal novel, hypothesis-generating, gene association patterns in the context of targeted subcellular location.

Keywords: Sitka spruce; adaptation mechanisms; carbon metabolism; cell walls; microarray; visualization

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