Welcome to MultiOmicsXplorer!

This tool analyzes phosphoproteomic, proteomic, and transcriptomic data from various types of tumors at different stages, allowing comparisons between tumors and stages.

In the OncoXplorer-CPTAC Data Analysis section, you can compare tumor data from the CPTAC portal across different stages and tumor types.

The Extract Protein Activity from Your Data section allows you to use SignalingProfiler to extract protein activity uploading your data.

Click here for the tutorial to learn how to use the app.

CPTAC data

Data Processing and Harmonization

We use data that have been downloaded using the tutorial described in the following paper:

Simplified and Unified Access to Cancer Proteogenomic Data

We collected clinical data - used to obtain information about the tumors stages, and raw transcriptomics proteomics and phosphoproteomics data.

Pre-processing Steps

The raw data underwent several filtering and transformation steps to ensure consistency and usability:

  • Transcriptomics: Filtered out rows with more than 80% zero values and removed non-coding elements.
  • Proteomics: Updated protein identifiers to match Uniprot ID.
  • Phosphoproteomics: Updated Uniprot ID and sequence window based on the phosphorylated residue.

Harmonization Process

To standardize the data across different omics layers, we applied the following transformations:

  • Missing values (NA) in proteomics and phosphoproteomics data were imputed.
  • Z-score normalization was applied to all three omics datasets to facilitate comparisons.

If you need to harmonize your data, you can easily access the PatientProfiler package (Lombardi et al., 2025)

Remember to click this button every time to update the plot and the table.
Download plot (PDF) 

                          

                        

                      

                    

                    

                      

                      

                        
                        

                          
                          
                        

                      

                      
                        
                        Download data
                      
                    

                  

                

                

                  

                    

                      

                        
                        

                          
                          
                        

                      

                      

                        
                        

                          
                          
                        

                      

                      

                        

                          
                          

                            
                            
                          

                        

                        

                          
                          

                            
                            
                          

                        

                      

                      

                        

                          
                          

                            
                            
                          

                        

                        

                          
                          

                            
                            
                          

                        

                      

                      

                        

                          
                        

                      

                      

                        

                          
                        

                      

                      

                        
                        

                          
                          Remember to click this button every time to update the plot and the table.
                        

                      

                    

                    

                      

                        

                          

                            
                            
                              
                              Download plot (PDF)
                            
                          

                        

                      

                    

                    

                      

                      

                        
                        

                          
                          
                        

                      

                      
                        
                        Download data
                      
                    

                  

                

              

            

          

          

            

              
              

                

                  

                    SignalingProfiler Tool
                  

                  

                    

                      
This application uses the SignalingProfiler pipeline to perform protein activity inference as described in the following paper:

                      SignalingProfiler: A Tool for the Quantitative Analysis of Proteomics Data (Venafra V., Sacco F., Perfetto L., 2024)
                      

                      Click here to access the complete tutorial
                      

                      
The following three sample dataframes are provided to illustrate the proper format for providing omics dataframes to input to SignalingProfiler.

                      
To ensure analysis, the columns must be renamed as they are in the examples.

                      
All three omics dataframes can be loaded to initiate the analysis, or if one or two are missing, the analysis will be performed in the most optimal way based on the loaded dataframe(s).

                      
Transcriptomics Data Example

                      

                      

                      
Proteomics Data Example

                      

                      

                      
Phosphoproteomics Data Example

                      

                    

                    

                      
                    

                  

                

                

                  

                    

                      
Upload data for one or multiple samples

                      

                        Note: File names should follow the pattern 
                        P_<ID>
                         for proteomics, 
                        Ph_<ID>
                         for phosphoproteomics, and 
                        T_<ID>
                         for transcriptomics. For example, if the sample ID is 
                        C3L00010
                        , you should name the proteomics file: 
                        P_C3L00010.tsv or .csv or .xlsx
                      

                      

                        
                        

                          
                          
                        

                        

                          

                        

                      

                      
⚠️ Warning: Please ensure your data contains columns in the order shown in the previous section.
                                    
 In addition, it is also important to have in your data correct UniProt IDs and valid amino acids (S, T, or Y). 
                                    Otherwise, the data will undergo a partial cleanup and some entries might be removed.

                                    For proper data preprocessing, refer to the PatientProfiler package.

                      

                      

                        
                        

                          
                          

                            
                            
                          

                        

                        

                          
                          Select Human or Mouse to apply organism-specific regulatory models during activity inference.
                        

                      

                      

                        
                        

                          

                            
                          

                          

                            
                          

                        

                      

                      

                        
                        

                          
                          
This will clear all current data and results. You'll need to re-upload the files before running a new analysis.

                        

                      

                      

                        
                        Press 'Clear Data' before starting a new analysis.
                      

                      

                        

                        
TF Activity Footprint Analysis

                        

                          
                          
                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                        
Kinase-Phosphatase Activity Footprint Analysis

                        

                          
                          
                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                        
PhosphoScore Computation

                        

                          

                            
                          

                        

                        

                          

                            
                          

                        

                        

                      

                    

                    

                      

                        

                          

                            
Protein Activity Inference Results

                            
                            
                            
Once you have obtained the results, you can use them in the 'Plot Results' section to visualize the data.

                            

                            
Summary Table

                            
                            
                            

                            

                            

                          

                        

                      

                    

                  

                

                

                  
View the Top 15 Up and Down-Regulated Proteins Based on Their Predicted Activity

                  
Here you can upload your results from the protein activity inference to visualize your data 
                           in a barplot, separated by molecular function.

                  

                    
                    

                      
                      
                    

                    

                      

                    

                  

                  

                    
                    

                      

                        
                      

                      

                        
                      

                    

                  

                  
(Selecting 'All Samples' will show the mean predicted activity across your cohort)

                  

                  
                  
                    
                    Download Plot
                  
                  

                  
                  

                  

                    Molecular Functions (mf):
                    
    
                      
  • tf: Transcription Factor
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  • kin: Kinase
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  • phos: Phosphatase
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  • other: Other
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📘 Help and Documentation

                

                
❓ Common Issues

                
    
                  
  • 
                    Q:
                     I can't see the plots after selecting the analytes.
                    
    
                    A:
                     Make sure you have selected at least one tumor and one stage. Also, ensure that the data for the selected analyte is available.
                  
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  • 
                    Q:
                     The data download button is not working.
                    
    
                    A:
                     Please check your internet connection and ensure that your browser allows downloads.
                  
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💡 Tutorial

                

                  For a detailed tutorial on how to use MultiOmicsXplorer, please visit: 
                  MultiOmicsXplorer Tutorial
                

                

                
📨 Contact Information

                
For further assistance or inquiries, feel free to contact us:

                
    
                  
  • PerfettoLab of Bioinformatics, University of Rome "La Sapienza"
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  • Head of the Lab: Dr. Livia Perfetto
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  • Primary curator of MultiOmicsXplorer: Dr. Eleonora Meo
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  • 
                    Email: 
                    eleonorameo.hp@gmail.com
                  
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🔬 About the Lab

                
PerfettoLab specializes in bioinformatics research and analysis, with a focus on cancer genomics and proteomics. 
                     We are dedicated to developing tools like MultiOmicsXplorer to facilitate data analysis for cancer research.

                

                  Visit our website: 
                  PerfettoLab Homepage