Visualising gene expression in its metabolic context.
Relative changes in mRNA as well as protein levels induced by sublethal doses of antibiotics on bacteria are measured and results visualised in the context of metabolic pathway diagrams. The mRNA levels present at a given time point after the addition of the antibiotic are measured using microarrays from Affymetrix. Additionally, the relative amount of each protein synthesised during 3 minute intervals sampled at the given times is measured using radio-labelling followed by two-dimensional polyacrylamide gel electrophoresis and the subsequent analysis of the images produced by exposure to a phosphorimager. Metabolic pathway diagrams are both constructed in-house and imported from KEGG (Kyoto Encyclopedia of Genes and Genomes). Both protein and mRNA expression data can be displayed in the pathway diagrams such that the colour of the vectors or enzyme identifiers indicate the relative change in expression level and reproducibility.
Wolf
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F. Hoffmann-La Roche Ltd, Basel, Switzerland. Detlef.Wolf@Roche.com
Gray
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CP
de Saizieu
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D019295:Computational Biology; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D006193:Haemophilus influenzae / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D020543:Proteome; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012984:Software; D013296:Streptococcus pneumoniae / Q000235:genetics / Q000378:metabolism
D020543:Proteome; D012329:RNA, Bacterial; D012333:RNA, Messenger