Open Access Highly Accessed Research article

Adapted Boolean network models for extracellular matrix formation

Johannes Wollbold12*, René Huber34, Dirk Pohlers3, Dirk Koczan5, Reinhard Guthke1, Raimund W Kinne3 and Ulrike Gausmann6

Author Affiliations

1 Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany

2 Institute of Algebra, Technische Universität Dresden, Zellescher Weg 12-14, 01062 Dresden, Germany

3 Experimental Rheumatology Unit, Department of Orthopaedics, University Hospital Jena, Friedrich Schiller University Jena, Klosterlausnitzer Str. 81, 07607 Eisenberg, Germany

4 Institute of Clinical Chemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany

5 Proteome Center Rostock, University of Rostock, Schillingallee 69, 18055 Rostock, Germany

6 Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstr.11, 07745 Jena, Germany

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BMC Systems Biology 2009, 3:77  doi:10.1186/1752-0509-3-77

Published: 21 July 2009

Additional files

Additional file 1:

Literature used for the network construction. Each citation corresponds to one edge in the regulatory network.

Format: DOC Size: 367KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 2:

Cytoscape import file. Import this file into Cytoscape [http://www.cytoscape.org/ webcite] to analyse the gene regulatory network in more detail. It also includes external links for the genes and references cited to GenBank, Uniprot, and PubMed.

Format: ZIP Size: 18KB Download file

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Additional file 3:

Cytoscape import file. Open this file after importing the CYS (file provided by Additional file 2) into Cytoscape [http://www.cytoscape.org/ webcite] if the layout of the CYS file cannot be displayed correctly with your Cytoscape version.

Format: ZIP Size: 5KB Download file

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Additional file 4:

List of probe sets used, processed microarray data, and visualisation of expression time courses for the genes analysed. Raw data are deposited under accession number GSE13837 at http://www.ncbi.nlm.nih.gov/geo/ webcite.

Format: XLS Size: 640KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 5:

Processed and visualisation of GEO Data. Data were extracted from GSE1742 (TGFβ1) and GSE2624 (TNFα) at http://www.ncbi.nlm.nih.gov/geo/ webcite.

Format: XLS Size: 157KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 6:

Discretised gene expression time courses. For the discretisation method, see Results and Discussion as well as Methods sections.

Format: XLS Size: 45KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 7:

Histograms of gene expression simulation. The simulations for TGFβ1 (blue) and TNFα (red) were run for 12 time steps (x-axis) and for each initial state derived from the patients' data separately. A simulated expression of 100% (y-axis) means that in all six cases the gene was on.

Format: XLS Size: 204KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 8:

List of the top 500 occurring KN rules. Excel file containing the top 500 knowledge base rules valid for the simulations as well as for the data from stimulations with TGFβ1 and TNFα.

Format: XLS Size: 1.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 9:

Temporal rules after TGFβ1 stimulation. Complete lists, valid for the simulation and the observed time series.

Format: TXT Size: 413KB Download file

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Additional file 10:

Temporal rules after TNFα stimulation. Complete lists, valid for the simulation and the observed time series.

Format: TXT Size: 1.1MB Download file

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Additional file 11:

Temporal rules after TGFβ1 stimulation in PROLOG format. E.g., for the use with the XSB Logic Programming and Deductive Database system, supporting tabled resolution http://xsb.sourceforge.net/ webcite.

Format: TXT Size: 729KB Download file

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Additional file 12:

Temporal rules after TNFα stimulation in PROLOG format. E.g., for the use with the XSB Logic Programming and Deductive Database system, supporting tabled resolution http://xsb.sourceforge.net/ webcite.

Format: TXT Size: 1.5MB Download file

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