This article is part of the supplement: Proceedings of the Fourth Annual MCBIOS Conference. Computational Frontiers in Biomedicine
Proceedings
Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis
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* Corresponding author: Robert E Hurst Robert-Hurst@ouhsc.edu
1 Department of Urology, College of Medicine, Oklahoma University Health Sciences Center, PO Box 26901, Oklahoma City, OK 73190, USA
2 Department of Physiology, College of Medicine, Oklahoma University Health Sciences Center, PO Box 26901, Oklahoma City, OK 73190, USA
3 Department of Biochemistry and Molecular Biology, College of Medicine, Oklahoma University Health Sciences Center, PO Box 26901, Oklahoma City, OK 73190, USA
4 Department of Pharmaceutical Sciences, College of Pharmacy, Oklahoma University Health Sciences Center, PO Box 26901, Oklahoma City, OK 73190, USA
5 Department of Environmental Health Sciences, College of Public Health, Oklahoma University Health Sciences Center, PO Box 26901, Oklahoma City, OK 73190, USA
6 Microarray Core Facility, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
BMC Bioinformatics 2007, 8(Suppl 7):S2 doi:10.1186/1471-2105-8-S7-S2
Published: 1 November 2007Additional files
Additional file 1:
Confocal microscopy revealing the amount of cell death at different time points. A) Green – live HUC cells expressing GFP, red – dead HUC cells stained with propidium iodide. B) Cross section of HUC cells expressing dsRED and bacteria expressing GFP on top.
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Additional file 2:
Full list of 239 VHV genes in different clusters. GenBank accession numbers, gene names and description provided.
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Additional file 3:
Expanded versions of K-means and PAINT clustering of VHV genes showing gene names and GenBank accession numbers.
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Additional file 4:
Additional plausible network 2 in cluster 1. Hypothetical networks identified by Ingenuity© as being potentially present were pruned to remove genes that were not identified as being expressed.
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Additional file 5:
Additional plausible network 3 in cluster 1.
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Additional file 6:
Additional plausible network 4 in cluster 1.
Format: JPG Size: 1.3MB Download file
Additional file 7:
Additional plausible network 5 in cluster 1.
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Additional file 8:
Additional plausible network 6 in cluster 1.
Format: JPG Size: 625KB Download file
Additional file 9:
Plausible network for Cluster 2, 1 hour post infection, up-regulated
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Additional file 10:
Plausible network for Cluster 3, 1.5 hours post infection, up-regulated
Format: JPG Size: 777KB Download file
Additional file 11:
Plausible network for Cluster 4, 1.5 hours post infection, down-regulated
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Additional file 12:
Plausible network for Cluster 5, 4 hours post infection, up-regulated
Format: JPG Size: 774KB Download file
Additional file 13:
Plausible network for Cluster 6, 4 hours post infection, down-regulated
Format: JPG Size: 798KB Download file
Additional file 14:
Plausible network for Cluster 8, 8 hours post infection, up-regulated
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Additional file 15:
Plausible network for Cluster 9, 8 hours post infection, down-regulated
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Additional file 17:
Full list of 192 HV genes in cluster 1. GenBank accession numbers, gene names and description provided.
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Additional file 18:
Genes from expanded cluster 1 assembled in networks and their top functions/canonical pathways. Gene names in bold are "focus genes" identified from clusters formed from VHV genes. Non-expressed genes were manually removed from the networks. Statistically significant top functions and canonical pathways are identified by IPA.
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