Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Paul Grosu*, Jeffrey P. Townsend*†, Daniel L. Hartl†and Duccio Cavalieri*‡
Online Supplementary Information, Part2
Pathway Processor for B. subtilis.
We have developed a version of Pathway Processor modified to analyze data from Bacillus subtilis array experiments. We have applied the B.subtilis version to analyze one experiment from the paper from Price et al 2001. (Price, C.W., Fawcett, P., Ceremonie, H., Su, N., Murphy, C.K., Youngman, P. Genome-wide analysis of the general stress response in Bacillus subtilis. Mol Microbiol 2001 41:757--74).
The experiment studies the response to growth-limiting stresses, governed by the sigma(B) transcription factor. The dataset analyzed compares the transcriptional profiles of wild and mutant strains under ethanol-induced sigma (B) activity. Macroarrays representing more than 3900 annotated reading frames of the B. subtilis genome were hybridized to (33) P-labelled cDNA populations derived from wild-type and a sigB mutant strain that had been subjected to ethanol stress. In our analysis we compare the normalized dataset for the wild type exposed for 15 minutes to ethanol versus the normalized datasets for the sigma mutant exposed to 15 minutes ethanol.
The file that we used here can be downloaded at
Pathway processor predicts that the sigma mutant will show significant alterations in the following pathways: Peptidoglycan biosynthesis map550, ABC transporters map2010, Aminosugars metabolism map530, Fructose and mannose metabolism map51, Inositol phosphate metabolism map562.
This result is highly consistent with the analyses from Price et al., who observed variation in the relative message levels for known or predicted proteins regulating or encoding transporters controlling solute influx and efflux, including potential drug efflux pumps, such as the ABC transporter, and for products implicated in carbon metabolism, or envelope function.
The Expression mapper analysis of map 550 shows how deletion of the sigma factor affects the activation of the ethanol response genes involved in peptidoglycan biosynthesis, demonstrating that these genes are controlled by sigma B.
Files
Folder name. Pathway_processor_Bs.
Description
Contains the program Pathway Processor for B. subtilis.
File name Table3.xls
Description.
Table3 shows the sorted results of selected Signed Fisher Exact Test analyses for the comparison .
File name Map_550.tif
Description.
Map550. Expression Mapper output for Peptidoglycan biosynthesis in B. subtilis comparing the 2 normalized dataset for the sigma mutant exposed to ethanol versus the 2 normalized datasets for the wild type exposed to ethanol.
The text is colored in red if the relative change in gene expression is 1 or green if it is 1. The intensity of the color is proportional to the magnitude of the differential expression. The presence of a gray box indicates that the corresponding step in the biochemical pathway requires multiple gene products.
File name: PriceEtAlData.txt
Description. This file contains the data used to calculate the ratio and run pathway processor.
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