jdrudolph / photon

PHOsphoproteomic dissecTiOn using Networks

PHOTON is available as part of the Perseus software for proteomics analysis starting from Perseus version 1.6.2.1.

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.

Pubmed link

Intallation and Tutorial

Follow the installation instructions and learn how to use PHOTON from within Perseus.

Formulas

Please feel free to ask questions on the code and formulas used. Here you can find more detailed information.

Troubleshooting

Please open an issue here, or contact me directly if you have issues with installing or using PHOTON.

Licence

If the current licence does not suit your needs, please contacte me for alternative licencing options.

Contiribute

Constributions to the code and the documentation of PHOTON are welcome!

photon's Issues

Perseus-PHOTON exsample data

Hi, I'm just starting to learn to using the PHOTON. I download the phosphoSTY_rudolph.txt and load it into Perseus and follow the Data preparation wokflow.

what is the data type of the first four columns of this data? Are the first two columns the fold changes of EGF related experimental group relative to the control group? If so, how does the fold changes to be calculated? Is the quantitative value of each experimental group divided by the average value of the control group？

Thank you for your contribution and hope to answer my confusion.

PHOTON Web server gives an ANAT error while ANAT Cytoscape plugin works OK

I installed PHOTON with Docker, opened http://localhost:5000/, Downloaded the sample data, selected the sample data, set anchor = 1950, and pressed submit.

The web server gives me the below error popup.

HTTPConnectionPool(host='anat.cs.tau.ac.il', port=80): Max retries exceeded with url: /AnatWeb/AnatServer (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f5737217470>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))

To check if ANAT server is working, I downloaded Cytoscape, selected and installed ANAT app, and made some query with successful results.

Can't change column type

Good day

I am fairly new to phosphoproteomics and started using PHOTON on my university's PC recently. I am now trying to get Perseus and PHOTON to run on my personal PC as well, first trying the PHOTON tutorial data, however today I encountered an interesting error.
The error occurs right at the start when I try to change the column type of the combined_score column to Numerical. And most frustatingly, the error appears on both my home PC and my PC at the university, where I tried to check wether it was specific to one PC, but it was not.

(For non-German-speakers, the error reads "Index was outside the bounds of the array. It cannnot be negative of smaller than the collection", roughly translated)
This does not look like a Perseus-specific error to me, however I figured someone might have run into this problem before and knows a solution.
I am most grateful for any help

-C

Is Perseus the only way to use photon?

Our package artMS supports the generation of the input files required originally by PHOTON when was not part of Perseus. I think Photon had a legacy option that we cannot find anymore. The question is:

Is Perseus / Windows officially the only way to use Photon? If so, we would remove the function that is currently available in our package to generate photon inputs. Alternatively, if there is any way that photon could be used outside of Perseus, we will be happy to support it.

Please, let me know. Thanks a lot

Photon - Value cannot be null

Hi Jan,

I'm trying to use the photon modification with the interactions tutorial data. I have setup my python path and it appears in the executable box as green. I keep getting an error message however, and I'm unsure where the issue is (see below).

Any help you can give me would be greatly appreciated!

Photon analysis

Hi,

I have a few questions concerning the analysis.

1)What is the format of the data input? I have label free phosphoproteomics from 2 groups : WT vs disease. Do I just use the log2FC column after doing a t-test between the groups and connect that to the network?
2)Once I have the network collection and matrix from Photon analysis, how do I know which proteins are affecting the phosphorylation the most? Do you just filter the Nodes with the signaling score? If I only want to see the kinases, is it right to add the Keywords annotations and filter these with kinases? What about the ones not detected in my dataset?
3)Is it possible to get a legend when visualising? I suppose the darker the node the more phosphorylated it is.
4)l haven't been able to find a tutorial for the KSEA analysis within Perseus. Is there any? if not would you have any tips (as I assume it is very similar to Photon, just need to create a different network).

Thanks heaps

Cheers,

Isaline

Issue with Generic network export

Hi Jan,

I can't reload the network that I exported from generic network export.

Issue during PHOTON reading parameter

Dear Jan Rudolph

Hello,

I have up to dated all packages even perseus and anaconda python, but during the PHOTON this error always come out. Could you have a look it and what is wrong? Please.

Best regards,

Sarkawt

Can not open the STRING Network for phosphoproteomic analysis

Dear Jan,

I am trying to do network analysis for phosphoproteomics accroding to the Youtube video of Perseus https://www.youtube.com/watch?v=svHRuH148QY&t=1560s
I used the newest version of Perseus, however, In was not able to connect to the PHOTON. After searching I realized that I need to use the older version of Perseus (1.6.14.0) to be able to connect to the PHOTON. Now there is another problem. In this vesrion (1.6.14.0) I am not able to get the STRING network from matrix and I get an error for that. Do you have any solution for that? I attached the error photo.

Thank you in advance,

Best regards,
Shayan Khozooei

excutor

Dear Rudolph,

I am new in the phosphoproteomics data analysis and I want to use PHOTON for one of my experiment. I follow all steps as you have explained in tutorial videos, and everything went fine, except at the end step when I run PHOTON this error always come out (joblib.external.loky.process_excutor.RemoteTraceback). I have no idea why this is always coming out when I have up to date everything.

Please, do you have any suggestion how to overcome this error?

Best regards,

Sarkawt

Data Input

Hi,

I am working with label free phosphoproteomics data, 2 genotypes (Disease-WT), 4 biological replicates per genotype.
Is it correct to use the log FC Disease/WT (one column) as the input data for Photon?
Thanks

Isaline

Output error following tutorial with Perseus

Hi,

At the step of performing the PHOTON analysis in Perseus, this output error is thrown (attached).

Any help/advice to resolve this would be great.

Cheers

Change PPI network

Hello Jan,

Did I understand it correctly that PHOTON is using the human PPI (see default.py)? If yes, is it possible for the user to change the files specified in default.py, preferably from a Windows machine?

Many Thanks,
Stephanie

Link to tutorial data appears broken

Hi-

I'm new to Perseus and Photon but trying to learn via your tutorial. However, the link to the example data on the tutorial page (https://github.com/jdrudolph/photon/blob/master/docs/Perseus/tutorial.md) appears broken.

-Cheers,
Jason

I always got error message while processing Photon.

Hi Jan,

Currently, I am trying to apply Photon to analyze some phosphoproteome data. But I always got this error message. Do you have any suggestions to solve this problem?

Thank you very much first
Best,
Juan

Phosphosite information

Hi,

I have a question about your tool, how did you store and use the phosphosite information?

Thanks!
Corinne

Unable to complete job

Description of output

Hi jdrudolph,
great software, might be rather useful! I wondered if you have a description of your outputs. I downloaded the output and got a GO_scores, predictions,.... file. I am particular confused about the prediction file.
Maybe I missed it, but do you have some sort of documentation for this?

Thanks a lot!
M

Error when using Python

Hi Jan,
I keep getting an error message after launching photon. I believe it is because there is a white space in the output path? Would you know how to fix this? Thanks !

Could not load type 'PerseusApi.Utils.PerseusFactory

Hello Jan,

I am trying to generate the network collection, following your tutorial. I have done all the processing on the matrices and everything looks fine, however, when I click "ok" after "basic"-> "from matrix" -> check "Network is directed", I get an error message saying "Could not load type 'PerseusApi.Utils.PerseusFactory'"! Am I missing some plug-in?

Thank you very much for your time!

windows server 2008

I tried to install the software on windows 2008 server, attached the error. how do I fix?

thanks
Andrea

Error on using custom data: Cannot have number of folds n_folds=10 greater than the number of samples: 3.

I get the above error when using my own data which looks like this (full dataset is longer):

GeneID	Amino.Acid	Position	avg	Symbol
1027	S	17	-1.96578	CDKN1B
1822	S	79	1.360083	ATN1
2353	S	36	1.306262	FOS
2353	S	364	1.306262	FOS
2886	S	7	0.897628	GRB7
2886	S	66	0.897628	GRB7
3607	S	42	-1.074	FOXK2
3607	S	424	-1.074	FOXK2
4008	S	159	1.146003	LMO7
4041	S	161	-5.64386	LRP5
4041	S	1609	-5.64386	LRP5
4082	S	17	-1.02915	MARCKS

Is there any documentation for Photon? I tried to figure out where this error could be coming from but I haven't been able to. The data is human.

Sorry if this is written somewhere but I've been making assumptions about exactly what the required information in the input files is and I should check with you if these are correct. I've been assuming that the 'avg' column is a log2 fold change, is this correct? Also is 'Symbol' supposed to be GENENAME as reported from here: http://www.uniprot.org/uploadlists/

A second, related data set gives the following error:

This solver needs samples of at least 2 classes in the data, but the data contains only one class: False

Any ideas?

Error after submitting data

When I try submit either a .csv or .txt file in the same format as the sample data using the browser, it gives:

"Internal Server Error: The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application."

Is there a way I can fix this?

Thanks.

any progress indicator available?

Hi,

I started Photon with a small dataset (128 phosphosites in some 80 proteins).
The job has been running for 20 hours (or so I see when using "docker ps" command)
Yet, in the browser I still see the message "working on job with id:....".

Could my job be hanging? How do I check the progress of my job?

Any suggestions will be appreciated,
Krzysztof

Find annotation file from UniProt to ENSP

Hello Jan!

I am following the turorial at https://github.com/jdrudolph/photon/blob/master/docs/Perseus/tutorial.md#phosphorylation-data and in step 3. I can't find the file mainAnnot.homo_sapiens.txt.gz. Where can I get it?

And also, I see in the paper that the application can run in a web browser interface independently of Perseus. How do you run it?

Best regards,
Francisco.

Error when running with custom data: 'DataFrame' object has no attribute 'to_frame'

Hi,
My docker installation runs fine with your sample data, but I get the above error when I try to use my own data. My data looks like this:

GeneID,Amino.Acid,Position,avg,Symbol
76707,S,1088,-0.997531494626,CLASP1
228140,S,429,-0.439277481319,TNKS1BP1
66922,S,186,0.988197913396,RRAS2
80288,S,21,0.00681367879271,BCL9L
80288,S,25,-0.894961248199,BCL9L
329877,S,1096,0.495977183684,DENND4C
71766,S,576,0.101136369347,RAVER1
16881,T,77,-0.387457567317,LIG1
226982,S,137,0.684338899602,EIF5B
68938,S,279,0.297268078714,ASPSCR1
21453,S,593,-0.933370239347,TCOF1
13178,S,11,0.610665511668,DCK

which seems to me to be the same format as your sample data, but I may have misinterpreted. Do you know what i'm doing wrong? many thanks, Sean

Can not find photon in Perseus

Dear Jan
I need to use photon and Perseus for my analysis. According to the installation guide, I have installed Photon and Perseus and python, but the photon is not available in my Perseus>Network>Modification.
Can you please help that how can I access it?
I attached a photo as well
Thank you very much

Is this tool still supported?

pip install photon_ptm won't install. Is this tool still supported?

PPI input data

Hi Jan!

I downloaded the data from http://cs.tau.ac.il/~jandanielr/db.tar.gz (see Dockerfile).
So my question is, what does each column in the ANAT file (H_sapiens.net) represent?

I would like to upload my own PPI network and I read this is possible (see issue #8) but first I am interested in gaining more experience with your own network.

Many thanks!
Best,
Jessica

Two of three sidedness options producing errors

The default, greater sidedness option works without producing an error, however the lesser sidedness option and two-sided options each produce a different error.
The lesser sided option produces the following error: no significant signaling functionality scores found, possibly due to insufficient data.
The two sided option produces the following error: side parameters has to be one of "greater", "twosided", "less", was two-sided.

Is this a glitch or can you suggest a possible solution for this problem?

Thanks,
Jonathan

Photon error

We are following the tutorial but are held up at one section where we are receiving an error when assigning the “from matrix” “source and target.” We have attached a screenshot of the error. Any help/suggestion would be most appreciated.

Thank you.

Error - Future Warning

Hello Jan,

While following the tutorial on another computer, I encountered another error message when I run PHOTON.

Also, when "Reconstruct signaling networks using ANAT" is unchecked, I get the "Value cannot be Null" error described by Laura.

Any help would be highly appreciated!
Best,
Michael

PHOTON-output issue

Hey,
I’m trying to do network analysis in Perseus (PHOTON), but I’ve run into a bunch of errors that are beyond my expertise.?
How can I deal with this error ?
Thank you for your time

Rawan

AttributeError: 'NoneType' object has no attribute 'text'

Dear Jan,

Recently I have tried to get Photon up and running within Perseus and I started with the tutorial dataset that was posted here as well. The tutorial is very clear, so thanks for that!

However, when I get to the very last stage (Actually performing the Photon analysis) I get the following error:

Any help is greatly appreciated!

All the best (and stay healthy ;)
Donna

PHOTON output error

Greetings,
I was running the PHOTON tutorial and ran into an output error (see attached). This is different than the other output error as my machine is running python 3.7.2. Any suggestions to help the program run would be appreciated.

Thanks,
Shawn

photon.error.pptx

Service Unavailable

Hello, this is Steven Guard from the University of Colorado Boulder. I am currently trying to run PHOTON using the tutorial dataset, but am unfortunately getting the following error:

b'\n\n<title>503 Service Unavailable</title>\n\n

Service Unavailable

\n

The server is temporarily unable to service your\nrequest due to maintenance downtime or capacity\nproblems. Please try again later.

\n

Additionally, a 503 Service Unavailable\nerror was encountered while trying to use an ErrorDocument to handle the request.

\n\n'

Is the server truly down at this moment, and if so when is it expected that this will be resolved?

Error message for network analysis

Hi!

I keep getting an error during step 2 in Create the PPI network from the edge table and prepare it for data annotation. I have the matrix of the protein-protein interactions open and am trying to transform it into the "Network collection" data structure by selecting Network → From matrix → Basic → From matrix and choosing protein1 and protein2 as 'Source' and 'Target', and checking the Network is directed option. When I click OK, I get the following error message:

I've tried installing the latest version of Perseus (v1.6.14.0) but the same error occurs. Any help would be much appreciated!

Container stopps working immediately

Hello Jan,

I try to get this container running for one of my scientifical colleagues. Unfortunately it immediately stopps working after starting it. I think the container does not find the run.sh script defined in the dockerfile:

ENTRYPOINT ["./run.sh"]

Errormessage:
docker: Error response from daemon: invalid header field value "oci runtime error: container_linux.go:247: starting container process caused \"exec: \\\"./run.sh\\\": stat ./run.sh: no such file or directory\"\n".

Do you have an idea how to fix it?

With Kind regards,

Christian

Cannot proceed through (Network → From matrix → Basic → From matrix)

Dear Jan,

I had a problem converting the StringDB PPI from matrix to network when following your tutorial on " Integrated network analysis of EGF and IGF stimulation using PHOTON". The Perseus version is 1.6.10.50. The error message is attached.

Thank you very much!
Min

processing fails at functional site prediction step

Hi, I have a couple of things to ask

1. I run the tool using proteins with only one ph site unequivocally detected in the protein, then photon crashes at the 4th step when the subnetwork has to be extracted. Is there any way to let it finish without having multiple sites per protein, i.e., add a checkpoint to either:

• skip that step of predicting functional sites even if there is only one in the protein or
• Still predict functional sites, even if there is only one in the protein.

2. Speaking of which, in order to see the 'progress report' I have to use the dev version of the container. When are you planning to make it the latest version?

Thanks and congratulation for the tool!