Research article
Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro
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* Corresponding author: Philip A Bronstein philip.bronstein@ars.usda.gov
1 United States Department of Agriculture-Agricultural Research Service, Robert W Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
2 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
3 Computational Biology Service Unit, Life Sciences Core Laboratories Center, Cornell University, Ithaca, NY 14852, USA
4 Department of Food Science, Cornell University, Ithaca, NY 14853, USA
BMC Microbiology 2008, 8:209 doi:10.1186/1471-2180-8-209
Published: 2 December 2008Additional files
Additional file 1:
Tables of differentially regulated genes. This Excel file contains tables of all differentially regulated genes identified with different p value cut-offs. Excel table of genes in the correct order from the pair-wise average linkage with un-centered correlation distance (Figure 5A) and the pair-wise average linkage with absolute un-centered correlation distance (Figure 5B).
Format: XLS Size: 528KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2:
p-0.01_average_uncentered_clustering.cdt. This CDT file can be used also with the accompanying GTR file to display the gene clustering of differentially regulated genes at GCRMA/FDR p = 0.01 using Java TreeView or similar viewer.
Format: CDT Size: 76KB Download file
Additional file 3:
p-0.01_average_uncentered_clustering.gtr. This GTR file can be used also with the accompanying CDT file to display the gene clustering of differentially regulated genes at GCRMA/FDR p = 0.01 using Java TreeView or similar viewer.
Format: GTR Size: 14KB Download file
Additional file 4:
p-0.01_average_absolute_uncentered_clustering.cdt. This CDT file can be used also with the accompanying GTR file to display the gene clustering of differentially regulated genes (without considering the direction of change) at GCRMA/FDR p = 0.01 using Java TreeView or similar viewer.
Format: CDT Size: 76KB Download file
Additional file 5:
p-0.01_average_absolute_uncentered_clustering.gtr. This GTR file can be used also with the accompanying CDT file to display the gene clustering of differentially regulated genes (without considering the direction of change) at GCRMA/FDR p = 0.01 using Java TreeView or similar viewer.
Format: GTR Size: 14KB Download file
Additional file 6:
Logos of RpoD and Fur motifs. This png file contains the sequence logos used to scan the DC3000 genome for putative gene targets of these regulators.
Format: PNG Size: 108KB Download file
