Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks
Phosphoproteomic experiments typically identify sites within a protein that are differentially phosphorylated between two or more cell states. However, the interpretation of these data is hampered by the lack of methods that can translate site-specific information into global maps of active proteins and signaling networks, especially as the phosphoproteome is often undersampled. Here, we describe PHOTON, a method for interpreting phosphorylation data within their signaling context, as captured by protein-protein interaction networks, to identify active proteins and pathways and pinpoint functional phosphosites. We apply PHOTON to interpret existing and novel phosphoproteomic datasets related to epidermal growth factor and insulin responses. PHOTON substantially outperforms the widely used cutoff approach, providing highly reproducible predictions that are more in line with current biological knowledge. Altogether, PHOTON overcomes the fundamental challenge of delineating signaling pathways from large-scale phosphoproteomic data, thereby enabling translation of environmental cues to downstream cellular responses.
Formulas
Please feel free to ask questions on the code and formulas used. Here you can find more detailed information.
Output description
A zip archive containing several output tables can be downloaded from the results page of PHOTON.
-
subnet.csv
: edges of the reconstructed signaling network. This is a sub-network of the input network (which is located at/db/anat/H_sapiens.net
). Thesubnet.csv
file can be e.g. imported into Cytoscape for further analysis. -
scores.csv
: signaling functionality scores devised by PHOTON. The 'Significant' column allows for easy filtering of the table. The other columns provide more detail on each step of the algorithm, i.e. calculating an empirical score, obtaining p-values, and finally FDR-corrected q-values. -
go_scores.csv
: details all GO annotation enrichment results for the reconstructed network. Filtering for the 'rejected' column (=1) will yield all sign. enriched categories. The naming of the other columns follows the convention of the statistical test used. -
predictions.csv
: contains information regarding the functional phosphorylation site prediction. The 'proba' column is the prediction score for each site. If the phosphorylation site was part of the training set the 'label' column will be 'TRUE'. One should take special care when the training set was small, i.e. few sites with 'label' set to TRUE are in the data set.
My result graph contains only a sigle node '-1'
Sometimes PHOTON will not yield any results. Known technical sources of failure are:
- The ANAT service is down. PHOTON relies on the ANAT web server which can be down for various reasons. Before reporting an error with PHOTON, please confirm that the Cytoscape plugin for ANAT is working as expected. Please note that you might still download the resulting activity scores derived by PHOTON.
Common errors when running PHOTON
-
Uploading a data file which is not
ASCII
encoded might yield errors such as'utf-8' codec can't decode byte 0xa0 in position 0: invalid start byte
Converting the file to
ASCII
will fix this issue. -
There is a popup with a long error message similar to
<ns2:confidence>0.6912981534952782</ns2:confidence> <ns2:fromNodeId>473</ns2:fromNodeId> <ns2:toNodeId>126961</ns2:toNodeId> </ns2:edgesData> <ns2:edgesData> ...
This error messages is due to the ANAT web server not being available. Please confirm that the Cytoscape plugin for ANAT is working as expected before reporting an error for PHOTON. Please contact me or the authors of ANAT in case of errors.
Running PHOTON through Perseus
Installation
- Download Perseus from here.
- Install Python.
- Install perseuspy and PHOTON by running
pip install photon_ptm
. - Download
PluginPHOTON
from the plugin store.
Usage
- Load the
H_sapiens.txt
file usingGeneric matrix upload
. - Filter the rows by
Confidence > 0.5
. - Create a network from the matrix.
- Load the experimental data.
- Annotate the nodes of the network with the experimental data.
- Run PHOTON from Network => Processing => Modifications => PHOTON.
- Use the full network for e.g. enrichment analysis. The reconstructed subnetworks can be visualized. Signaling functionality scores are reported in a separate table and can be used for clustering etc.
Running PHOTON on Docker
PHOTON runs inside a 'container' and therefore requires docker to run across all platforms. General information regarding the installation of docker can be found on the docker website.
Docker Toolbox (Windows, Mac)
First open the Docker Quickstart Terminal
. After initialization (can take some time),
denote the IP address of docker (under the whale image).
Now you can run PHOTON by entering:
docker run -d -p 5000:5000 jdrudolph/photon
Now you can access PHOTON from your browser under the IP address
of docker followed by colon and 5000. For example 192.168.0.100:5000
.
Alternatively you can lookup the IP address using docker-machine ip default
.
Docker for Windows / Linux
Open a Powershell (terminal in linux) and run:
docker run -d -p 5000:5000 jdrudolph/photon
Now you can access PHOTON from your browser.
Native Linux (Experts)
Consult the Dockerfile
on how to run PHOTON on Linux natively.
Stopping PHOTON
First list all running containers:
docker ps
Lookup the name of the container (last column) and stop it using
docker stop name_of_container
Updating PHOTON
New versions of docker can be downloaded by running
docker pull jdrudolph/photon
before issuing the run
command as shown above.
Troubleshooting
Please open an issue here, or contact me directly if you have issues with installing or using PHOTON.
Licence
If the current licencing (see LICENCE.txt
) does not suit your needs,
please contacte me for alternative licencing options.
PHOTON data format example
GeneID,Amino.Acid,Position,avg,Symbol
5097,S,962,-0.47417884405658556,PCDH1
5097,S,984,-0.6438018715183813,PCDH1
4300,S,522,-0.5172999908818245,MLLT3
81628,S,264,0.8682687511988673,TSC22D4
81628,S,279,2.684096205546553,TSC22D4
4034,S,25,-0.593695490783283,LRCH4
4034,S,380,1.6585730683114723,LRCH4
6651,S,1822,0.046145203537912814,SON
6651,S,1737,-0.06153405253207198,SON