Title
Multivariate analysis of microarray data by principal component discriminant analysis: Prioritizing relevant transcripts linked to the degradation of different carbohydrates in Pseudomonas putida S12
Author
van der Werf, M.J.
Pieterse, B.
van Luijk, N.
Schuren, F.
van der Werff van der - Vat, B.
Overkamp, K.
Jellema, R.H.
TNO Kwaliteit van Leven
Publication year
2006
Abstract
The value of the multivariate data analysis tools principal component analysis (PCA) and principal component discriminant analysis (PCDA) for prioritizing leads generated by microarrays was evaluated. To this end, Pseudomonas putida S12 was grown in independent triplicate fermentations on four different carbon sources, i.e. fructose, glucose, gluconate and succinate. RNA isolated from these samples was analysed in duplicate on an anonymous clone-based array to avoid bias during data analysis. The relevant transcripts were identified by analysing the loadings of the principal components (PC) and discriminants (D) in PCA and PCDA, respectively. Even more specifically, the relevant transcripts for a specific phenotype could also be ranked from the loadings under an angle (biplot) obtained after PCDA analysis. The leads identified in this way were compared with those identified using the commonly applied fold-difference and hierarchical clustering approaches. The different data analysis methods gave different results. The methods used were complementary and together resulted in a comprehensive picture of the processes important for the different carbon sources studied. For the more subtle, regulatory processes in a cell, the PCDA approach seemed to be the most effective. Except for glucose and gluconate dehydrogenase, all genes involved in the degradation of glucose, gluconate and fructose were identified. Moreover, the transcriptomics approach resulted in potential new insights into the physiology of the degradation of these carbon sources. Indications of iron limitation were observed with cells grown on glucose, gluconate or succinate but not with fructose-grown cells. Moreover, several cytochrome- or quinone-associated genes seemed to be specifically up- or downregulated, indicating that the composition of the electron-transport chain in P. putida S12 might change significantly in fructose-grown cells compared to glucose-, gluconate- or succinate-grown cells. © 2006 SGM.
Subject
Biology
Biotechnology
bacterial RNA
cytochrome
fructose
gluconic acid
glucose
glucose dehydrogenase
iron
quinone derivative
succinic acid
article
bacterial gene
bacterium culture
carbohydrate metabolism
carbon source
cluster analysis
controlled study
discriminant analysis
down regulation
fermentation medium
fructose metabolism
gene identification
genetic transcription
glucose metabolism
intermethod comparison
metabolic regulation
microarray analysis
molecular cloning
multivariate analysis
nonhuman
plots and curves
principal component analysis
priority journal
Pseudomonas putida
regulatory mechanism
respiratory chain
RNA analysis
RNA isolation
transcriptomics
upregulation
Carbohydrate Metabolism
Culture Media
Genes, Bacterial
Multivariate Analysis
Oligonucleotide Array Sequence Analysis
Pseudomonas putida
Bacteria (microorganisms)
Pseudomonas putida
To reference this document use:
http://resolver.tudelft.nl/uuid:036ca395-f000-4d8f-9bbc-259240ac4344
DOI
https://doi.org/10.1099/mic.0.28278-0
TNO identifier
239072
ISSN
1350-0872
Source
Microbiology, 152 (1), 257-272
Document type
article