Open Access Highly Accessed Research article

In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism

Srilatha Kuntumalla1, Quanshun Zhang2, John C Braisted1, Robert D Fleischmann1, Scott N Peterson1, Arthur Donohue-Rolfe2, Saul Tzipori2 and Rembert Pieper1*

  • * Corresponding author: Rembert Pieper rpieper@jcvi.org

  • † Equal contributors

Author Affiliations

1 Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

2 Division of Infectious Diseases, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA

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BMC Microbiology 2011, 11:147  doi:10.1186/1471-2180-11-147

Published: 24 June 2011

Additional files

Additional file 1:

Table S1. Protein abundance estimates from APEX quantitation. APEX abundance values of 1761 S. dysenteriae serotype 1 (SD1) in vitro and in vivo proteins quantitated at a <5% false discovery rate using the APEX Quantitative Proteomics Tool are listed along with their pi, ni, and Oi values. The corresponding gene names, locus tags, physicochemical properties and subcellular localizations are also listed in the table.

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Additional file 2:

Table S2. SD1 differential protein expression statistical analysis using Z-test and SAM. SD1 proteins listed in blue are upregulated under in vitro conditions. For the two tailed Z-test, SD1 proteins differentially expressed at 99% confidence are listed; for the two class SAM test, proteins differentially expressed at <10% FDR are listed.

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Additional file 3:

Table S3. APEX abundance values of SD1 in vitro and in vivo biological replicates. Three biological replicates from both in vitro and in vivo SD1 groups were analyzed as three to five technical replicates to expand the scope of the analysis; their APEX abundance values are listed.

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