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Open Access Highly Accessed Research article

Global analysis of the eukaryotic pathways and networks regulated by Salmonella typhimurium in mouse intestinal infection in vivo

Xingyin Liu1, Rong Lu1, Yinglin Xia2 and Jun Sun134*

Author Affiliations

1 Department of Medicine, Gastroenterology & Hepatology Division, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA

2 Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA

3 Department of Microbiology and Immunology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA

4 Wilmot Cancer Center, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA

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BMC Genomics 2010, 11:722  doi:10.1186/1471-2164-11-722

Published: 20 December 2010

Additional files

Additional file 1:

Primer sequence for qRT-PCR. Listing all primer sequences used in qRT-PCR (PDF file). PCR data were shown in Figure 6C, 7C, and Figure 9.

Format: PDF Size: 421KB Download file

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Additional file 2:

The list of differentially expressed genes between the control and 8 hours post-infection groups. Listing differentially expressed genes (fold times ≥ 1.2; P < 0.05) at 8 hours post-infection comparing with the control group without Salmonella infection.

Format: XLSX Size: 71KB Download file

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Additional file 3:

The list of differentially expressed genes between the control and at 4 days post- infection groups. At 4 days post-infection, differentially expressed genes are listed in Table S3.

Format: XLSX Size: 519KB Download file

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Additional file 4:

The list of differentially expressed genes between the 8 hours and 4 days post- SL1344 infection. Identify genes that were expressed differentially during two time course.

Format: XLSX Size: 557KB Download file

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Additional file 5:

All pathways involved in colon mucosa 8 hours post-SL1344 infection. List pathways involved in colon mucosa with Salmonella infection at 8 hours.

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Additional file 6:

The gene list for Network 1, NF-kappaB. List genes interact directly with NF-kappaB transcription factor.

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Additional file 7:

Networks of interacting up-regulated genes at 8 hours post-infection. Identify 14 highly significant networks of potentially interacting up-regulated genes at 8 hours post-infection group.

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Additional file 8:

Down-regulated genes 8 hours post-infection. Identify 16 highly significant networks of potentially interacting down-regulated genes and did not identify a network with center regulation.

Format: XLS Size: 29KB Download file

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Additional file 9:

All signaling pathways involved in colon mucosa with Salmonella infection at 4 days. List canonical pathways involving signaling associated with differential genes at 4 days post infection.

Format: XLS Size: 94KB Download file

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Additional file 10:

Canonical pathways changed by SL1344 infection. Figures for representative pathways involving signaling associated with Salmonella infection. Figure S1 EGF signaling; Figure S2 IL-9; Figure S3: Metabolic pathways; Figure S4: Top canonical signaling. Figure S5: co-regulated pathway between 8 hours and 4 days post-infection. Figure S6: Antigen presentation pathway; Figure S7: Interferon signaling; and Figure S8: IL-4 signaling.

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Additional file 11:

All metabolism pathways involved in colon mucosa with Salmonella infection at 4 days. All metabolism pathways involved in colon mucosa with Salmonella infection at 4 days.

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Additional file 12:

All metabolic pathways involved in colon mucosa with these differentially expression gene between 8 hr post-infection and 4 day post-infection. List the metabolism pathways involved in mucosa infection with these differentially expression gene between 8 hr post-infection and 4 day post-infection (fold times ≥ 1.2 times, p-value < 0.05).

Format: XLS Size: 44KB Download file

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Additional file 13:

Networks of interacting genes from amongst the up-regulated genes at 4 days post-infection. Identify highly significant networks of interacting genes from amongst the up-regulated genes at 4 days post-infection.

Format: XLS Size: 35KB Download file

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Open Data

Additional file 14:

Networks of interacting genes from amongst the down-regulated genes at 4 days post-infection. Identify highly significant networks of interacting genes from amongst the down-regulated genes at 4 days post-infection.

Format: XLS Size: 33KB Download file

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Additional file 15:

The gene list for Network 2. Network 2 presents IFN-γ in central positions and consists of 35 DEGs genes that are all regulated positively by IFN-γ.

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Additional file 16:

The gene list for Network 3. The network TNF-α in central positions and consists of genes that are all positively regulated by TNF-α.

Format: XLS Size: 32KB Download file

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Additional file 17:

The gene list for Network 4. The network 4 in central positions and consists genes that are all positively regulated by NR3C1.

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Additional file 18:

Common up-regulated genes function in both early stage and late stage of infection. Identity commonly up-regulated in response to Salmonella infection at the early and late stage of infection.

Format: XLS Size: 25KB Download file

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Additional file 19:

Functional categories associated with common up-regulated genes. Identify the top functional categories associated with these common up-regulated genes.

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Additional file 20:

Common down-regulated genes function in both early stage and late stage of infection. Identity commonly down-regulated in response to Salmonella infection at the early and late stage of infection.

Format: XLS Size: 51KB Download file

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Additional file 21:

Functional categories associated with common down-regulated genes. Identify the top functional categories associated with these common down-regulated genes.

Format: XLS Size: 25KB Download file

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Additional file 22:

The gene list for EGFR signaling pathways at 4 days of post-infection. EGFR and downstream signaling proteins are involved in Salmonella infection.

Format: XLS Size: 36KB Download file

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Additional file 23:

The gene list for NRF2-mediated oxidative stress response signaling at 4 days of post-infection.

Format: XLS Size: 46KB Download file

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Additional file 24:

Antigen presentation pathway were up-regulated. the antigen processing pathway was activated by pathogenic Salmonella infection in colon mucosa.

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Additional file 25:

43 enzymes down-regulated at 4 days post-infection. 43 enzymes in the valine, leucine, and isoleucine degradation pathway were down-regulated at 4 days post-infection, including acetyl-Coenzyme A acyltransferase family member

Format: XLS Size: 32KB Download file

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Additional file 26:

The gene list for IL-4 signaling pathway at 4 days of post-infection. Identify genes associated with IL-4 at 4 days post-infection.

Format: XLS Size: 33KB Download file

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Additional file 27:

The gene list for IL-9 signaling pathway at 4 days of post-infection. Identify genes associated with IL-9 at 4 days post-infection.

Format: XLS Size: 28KB Download file

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