SignalingProfiler is a R based pipeline that integrates transcriptomics, proteomics and phosphoproteomics data among a case and a control to build a signaling network, connecting:

• cellular receptor(s);
• kinases and phosphatases;
• targets of phosphorylation;
• transcription factors;

This network provides mechanistics hypoteses about the remodeling of the signal due to your case.

To install SignalingProfiler execute the following command in R.

R >= 4.1 is required

devtools::install_github('https://github.com/SaccoPerfettoLab/SignalingProfiler/')

SignalingProfiler is currently under active development, as such we suggest to delete and re-install the package regularly to exploit the new features.

SignalingProfiler is dependent on Saez lab algorithm CARNIVAL for performing the signalling pathway optimization. You can find all the instruction for installation in Saez lab repository CARNIVAL.

The latest tutorial of SignalingProfiler is available here.

Old tutorials for human are available here and here.

You can find an example of SignalingProfiler analysis for mouse here.

If you use SignalingProfiler in your research please cite the latest publication and the first publication.

Venafra V, Sacco F, Perfetto L. SignalingProfiler 2.0 a network-based approach to bridge multi-omics data to phenotypic hallmarks. NPJ Syst Biol Appl. (2024). https://doi.org/10.1038/s41540-024-00417-6.

Massacci, G., Venafra, V., Latini, S. et al. A key role of the WEE1-CDK1 axis in mediating TKI-therapy resistance in FLT3-ITD positive acute myeloid leukemia patients. Leukemia (2022). https://doi.org/10.1038/s41375-022-01785-w