Systems biology approach for mapping the response of human urothelial cells to infection by -2

<p><b>Copyright information:</b></p><p>Taken from "Systems biology approach for mapping the response of human urothelial cells to infection by "</p><p>http://www.biomedcentral.com/1471-2105/8/S7/S2</p><p>BMC Bioinformatics 2007;8(Suppl 7):S2-S2.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2099488.</p><p></p> TREs for those genes, filtered by p < 0.05 and FDR < 0.3

Systems biology approach for mapping the response of human urothelial cells to infection by -1

<p><b>Copyright information:</b></p><p>Taken from "Systems biology approach for mapping the response of human urothelial cells to infection by "</p><p>http://www.biomedcentral.com/1471-2105/8/S7/S2</p><p>BMC Bioinformatics 2007;8(Suppl 7):S2-S2.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2099488.</p><p></p>ncrease/decrease in relative gene expression level referenced to the median of the gene over time, respectively. B) Common TREs for given clusters. Color bars at right represent different gene clusters. Red indicates genes sharing overrepresented (p < 0.05) TREs, grey/blue mark genes with not significantly overrepresented/underrepresented TREs, respectively. A larger version complete with gene names is provided in the Additional file . A schematic diagram of the significant functions identified by IPA can be found in Figure 5

Systems biology approach for mapping the response of human urothelial cells to infection by -0

<p><b>Copyright information:</b></p><p>Taken from "Systems biology approach for mapping the response of human urothelial cells to infection by "</p><p>http://www.biomedcentral.com/1471-2105/8/S7/S2</p><p>BMC Bioinformatics 2007;8(Suppl 7):S2-S2.</p><p>Published online 1 Nov 2007</p><p>PMCID:PMC2099488.</p><p></p>am is superimposed on the actual histogram. SD – standard deviation for the normal distribution, 3*SD (white vertical line) – cut-off level for HV genes, red vertical line – cut-off for VHV genes with relative SD ≥ 0.2

Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation-14

<p><b>Copyright information:</b></p><p>Taken from "Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation"</p><p>http://www.biomedcentral.com/1471-2172/8/17</p><p>BMC Immunology 2007;8():17-17.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2000913.</p><p></p>tide are represented

Representative photomicrograph of the mouse bladder urothelium isolated and stained with DAPI and secondary antibody

<p><b>Copyright information:</b></p><p>Taken from "Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation"</p><p>http://www.biomedcentral.com/1471-2172/8/17</p><p>BMC Immunology 2007;8():17-17.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2000913.</p><p></p

Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation-1

<p><b>Copyright information:</b></p><p>Taken from "Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation"</p><p>http://www.biomedcentral.com/1471-2172/8/17</p><p>BMC Immunology 2007;8():17-17.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2000913.</p><p></p>ptide are represented

Representative photomicrograph of the expected morphology of the urinary bladder in a cross-section

<p><b>Copyright information:</b></p><p>Taken from "Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation"</p><p>http://www.biomedcentral.com/1471-2172/8/17</p><p>BMC Immunology 2007;8():17-17.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2000913.</p><p></p> Figure 5A is a composite of 18 H&E stained photomicrographs of the same cross-section at original magnification of 100× and illustrates the localization of the different layers: urothelium and submucosa, as well as the detrusor muscle. Black wavy line indicates the urothelium/submucosal layer. Figure 5B is a high magnification of the mouse bladder urothelium showing a multi-layered urothelium with apical umbrella cells (yellow arrow)

Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation-15

<p><b>Copyright information:</b></p><p>Taken from "Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation"</p><p>http://www.biomedcentral.com/1471-2172/8/17</p><p>BMC Immunology 2007;8():17-17.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2000913.</p><p></p>ummarized on Table 2

Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation-13

<p><b>Copyright information:</b></p><p>Taken from "Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation"</p><p>http://www.biomedcentral.com/1471-2172/8/17</p><p>BMC Immunology 2007;8():17-17.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2000913.</p><p></p>P, or control peptide. Twenty four hours after instillation, the bladders were removed, placed on ice with peptidase inhibitors, and the urothelium/submucosa was isolated. Nuclear extracts from the bladder mucosa were analyzed by protein/DNA combo arrays containing 345 unique consensus-binding sequences per array [34]. TF expression was normalized to its own background (defined by adjusting a mean = 0 and SD = 1 of the distribution of non-expressed TFs). For further analysis, data obtained after normalization of each profile to its own background were log-transformed with substitution of negative values by the minimal logarithmic value obtained within positive values. Next, a robust regression analysis was conducted on expressed TFs and only TF with a ratio > 3.0 between PAR and control are represented

Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation-12

<p><b>Copyright information:</b></p><p>Taken from "Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation"</p><p>http://www.biomedcentral.com/1471-2172/8/17</p><p>BMC Immunology 2007;8():17-17.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2000913.</p><p></p>scribed in methods. Mice were euthanized 24 hours after the last instillation; the urinary bladders were removed rapidly, frozen, and shipped to Genpathway [40] for querying the chromatin for transcription of selected genes. After isolation, the chromatin was incubated with TFEB antibody to precipitate the CHIP DNA. The final CHIP DNAs were then used as templates in Q-PCR reactions, performed in triplicate, using specific primer pairs (Table 1). Results are presented as average and standard error of Transcription Binding Events Detected Per 1000 Cells. Asterisks indicate a statistical significant difference (p < 0.05) between a specific gene and the un-transcribed region used as control and a plus sign indicates a statistical significant difference (p < 0.05) between CHIPs isolated from PAR2-AP- and control peptide-treated bladders