The input files for this example come from the following papers:
- egfrdata1.phos and egfrdata2.phos Zhang et al, Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics,Proteomics, 2014 (doi: 10.1002/pmic.201400315)
- egfrdata3.phos Omerovic et al, Global Snapshot of the Influence of Endocytosis upon EGF Receptor Signaling Output, Journal of Proteome Research, 2012
The sample names are as follows:
- H3255_1_M.L:Tyrosine kinase inhibitor sensitive strain before stimulation with EGF
- H3255_1_H.M:Tyrosine kinase inhibitor sensitive strain after stimulation with EGF
- H1975_1_M.L:Tyrosine kinase inhibitor in-sensitive strain before stimulation with EGF
- H1975_1_H.M:Tyrosine kinase inhibitor in-sensitive strain after stimulation with EGF
- Endocytosis_A_H.L: (EGF+Dynasore)/Dynasore
- Endocytosis_B_M.L(EFG)/Dynasore : indicates EGF responsiveness
- Endocytosis_C_H.M (EGF+Dyn)/EGF: indicates Dynasore responsiveness of EGF-dependent signals
Parameters selected for this example include a cutoff of 2 for the Ratio cutoff and 3 for the Minimum Paths and the box for motif analysis has been selected. You can play around with additional parameters to get a better grasp at how SELPHI works.
The data input file 1, 2, 3 for this example comes from: Zhang et al, SILAC-based phosphoproteomics reveals an inhibitory role of KSR1 in p53 transcriptional activity via modulation of DBC1, BJC, 2013.For this example you will need the IDs map, the Database file and if you like to merge the replicates the file that defines how to merge the samples.
The source code will be made available as soon as the paper is accepted for publication