Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks
1 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
2 European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK, CB10 1SD
3 Immunology & Inflammation, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, 06877-0368, USA
4 Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
5 Merrimack Pharmaceuticals, Cambridge, MA, 02139, USA
BMC Systems Biology 2012, 6:29 doi:10.1186/1752-0509-6-29Published: 1 May 2012
Additional file 1:
Figure S1 Ensemble representation of TGFB, TNF, and WNT signalling networks. Alternate signal transmission routes connecting the extracellular ligands TGFB1 (A), TNF (B), and WNT (C) to their respective sentinel markers of pathway activity, SMAD4, NFKB1, and GSK3B. Shortest paths (i), and total number of paths as a function of path length (ii), color-coded by database source.
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Additional file 2:
Table S1 List of Pathways. S2 Gene Annotations. S3 Edge Annotations. S4 Pathway Gene sets.
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