Email updates

Keep up to date with the latest news and content from BMC Systems Biology and BioMed Central.

Open Access Highly Accessed Methodology article

Elementary signaling modes predict the essentiality of signal transduction network components

Rui-Sheng Wang1 and Réka Albert12*

Author Affiliations

1 Department of Physics, Pennsylvania State University, University Park, PA 16802, USA

2 Department of Biology, Pennsylvania State University, University Park, PA 16802, USA

For all author emails, please log on.

BMC Systems Biology 2011, 5:44  doi:10.1186/1752-0509-5-44

Published: 22 March 2011

Additional files

Additional file 1:

Algorithms developed and used in this study. This file contains the algorithms developed and used in this study, including the depth-first-search algorithm for enumerating all simple paths from the input node(s) to the output node(s) of a signaling network, the iterative integer linear programming algorithm for enumerating elementary signaling modes, the depth-first-search algorithm for estimating the number of elementary signaling modes, as well as the dynamic programming algorithm for finding shortest elementary signaling modes.

Format: PDF Size: 150KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Essentiality of the components from dynamic models of the three signaling networks. This file describes the essentiality of the signaling components obtained by dynamic simulation of Boolean models for the host immune response network and the guard cell ABA signaling network, and logical steady state analysis of the T cell receptor signaling network (Tables S1-S4).

Format: PDF Size: 202KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Essentiality of the guard cell ABA signaling components from our method. This file contains the importance values of the guard cell ABA signaling components obtained by single-node deletions (Figure S1) and two-node deletions (Figure S2), and literature support of the uncovered essential components.

Format: PDF Size: 109KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

The expanded T cell receptor signaling network. This file contains the expanded T cell receptor signaling network (Figure S3) and the importance values of the T cell receptor signaling components found by our method with AP as the input node (Figure S4).

Format: PDF Size: 414KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data