Email updates

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

Open Access Research article

From desk to bed: Computational simulations provide indication for rheumatoid arthritis clinical trials

Jennifer E Dent12 and Christine Nardini1

Author Affiliations

1 Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China

2 Population Health Research Centre, Division of Population Health Sciences and Education, St. George’s University of London, Cranmer Terrace, London, UK

BMC Systems Biology 2013, 7:10  doi:10.1186/1752-0509-7-10

Published: 22 January 2013

Additional files

Additional File 1:

Molecular-interaction map for RA. (a) protein-protein interaction map, (b) gene regulation map. The two maps are joined by transcription factors. For a more comprehensive view, we recommend to visualize the figure with CellDesigner [22].

Format: PDF Size: 8.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional File 2:

CRKL sub-network. Edges correspond to SBML reaction types: black - modifier; green - product; red - reactants. Reactions are labelled by a circle and species are labelled by a diamond.

Format: PDF Size: 47KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional File 3:

Mean expression level of network molecules for CRKL down-regulated. Simulated change in expression levels of a sample of molecules connected to CRKL, for low starting levels of CRKL (CRKL excluded). Sample chosen to display every 10th molecule, sorted by expression level at time t = 20.

Format: PDF Size: 171KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional File 4:

Mean expression level of network molecules for CRKL up-regulated. Simulated change in expression levels of a sample of molecules connected to CRKL, for high starting levels of CRKL (CRKL excluded). Sample chosen to display every 10th molecule, sorted by expression level at time t = 20.

Format: PDF Size: 172KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional File 5:

Mean expression level of network molecules significantly affected by regulation of CRKL. a) Simulated change in expression levels of molecules connected to CRKL, for CRKL down-regulated and b) Simulated change in expression levels of molecules connected to CRKL, for CRKL up-regulated. Nodes correspond to those in Table 1.

Format: PDF Size: 174KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional File 6:

Summary table of molecules. Summary of aliases, function and ontology (as described by GeneCard [31]) for molecules in Table 1.

Format: CSV Size: 45KB Download file

Open Data