Open Access Highly Accessed Methodology article

A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue

Walter K Schlage1, Jurjen W Westra2, Stephan Gebel1, Natalie L Catlett2, Carole Mathis3, Brian P Frushour2, Arnd Hengstermann1, Aaron Van Hooser2, Carine Poussin3, Ben Wong2, Michael Lietz3, Jennifer Park2, David Drubin2, Emilija Veljkovic3, Manuel C Peitsch3, Julia Hoeng3* and Renee Deehan2

Author Affiliations

1 Philip Morris International R&D, Philip Morris Research Laboratories GmbH, Fuggerstr.3, 51149 Koeln, Germany

2 Selventa, One Alewife Center, Cambridge, MA 02140, USA

3 Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland

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BMC Systems Biology 2011, 5:168  doi:10.1186/1752-0509-5-168

Published: 19 October 2011

Additional files

Additional file 1:

Tissue context origins for causal edges in the Cellular Stress Network. Corresponding tissue context categories are referenced in Figure 2.

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Additional file 2:

RCR-predicted hypotheses in the Cell Stress Network model. Indicates nodes that are RCR-predicted hypotheses from the four cell stress data sets analyzed (Hypoxia, OxPAPC, Hyperoxia, and HOCl). The building block(s) in which these nodes are contained is also shown in the rightmost column. See Additional File 10 for color and abbreviation key.

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Additional file 3:

Data set-derived nodes added to the Cellular Stress Network based on their predictions as hypotheses. See Additional File 10 for color and abbreviation key.

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Additional file 4:

Tables showing the nodes contained in each building block that comprise the Cellular Stress Network.

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Additional file 5:

Cellular Stress Network model colored for the HOCl data set. Red - node corresponds to observed increased mRNA; yellow halo - node is predicted by RCR to have increased activity; blue halo - node is predicted to have decreased activity.

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Additional file 6:

Cellular Stress Network model colored for the hyperoxia data set. Red - node corresponds to observed increased mRNA; green - node corresponds to observed decreased mRNA; yellow halo - node is predicted by RCR to have increased activity; blue halo - node is predicted to have decreased activity.

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Additional file 7:

Cellular Stress Network model colored for the hypoxia data set. Red - node corresponds to observed increased mRNA; green - node corresponds to observed decreased mRNA; yellow halo - node is predicted by RCR to have increased activity; blue halo - node is predicted to have decreased activity.

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Additional file 8:

Cellular Stress Network model colored for the OxPAPC data set. Red - node corresponds to observed increased mRNA; green - node corresponds to observed decreased mRNA; yellow halo - node is predicted by RCR to have increased activity; blue halo - node is predicted to have decreased activity.

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Additional file 9:

RCR-predicted Cellular Stress Network model hypotheses for the test data set comparisons. Hypotheses are grouped by pattern of prediction across the three test data set comparisons. See Additional File 10 for color and abbreviation key.

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Additional file 10:

Color and abbreviation key for hypothesis nodes.

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Additional file 11:

The Cellular Stress Network,.xls format.

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Additional file 12:

The Cellular Stress Network,.owl format. This file can be viewed using freely available network visualization software such as Cytoscape http://www.cytoscape.org/ webcite.

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