We use data that have been downloaded using the tutorial described in the following paper:
Simplified and Unified Access to Cancer Proteogenomic DataWe collected clinical data - used to obtain informations about the tumors stages, and raw transcriptomics proteomics and phosphoproteomics data.
The raw data underwent several filtering and transformation steps to ensure consistency and usability:
To standardize the data across different omics layers, we applied the following transformations:
If you need to harmonize your data, you can easily access the PatientProfiler package developed by Veronica Lombardi, Eleonora Meo and Veronica Venafra.
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)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).
Note: File names should follow the pattern below:
For example, if the sample ID is C3L00010 and you want to upload proteomics data, the file name should be: P_C3L00010.tsv/.csv/.xlsx.
Here you can upload your results from the protein activity inference to visualize your data in a barplot with a separation by molecular function.
(All Samples shows a mean for the predicted activity in your cohort)
Download PlotQ: I can't see the plots after selecting the analytes. What should I do?
A: Make sure you have selected at least one tumor and one stage. Also, ensure that the data for the selected analyte is available.
Q: The data download button is not working. What should I do?
A: Please check your internet connection and ensure that your browser allows downloads.
For further assistance or inquiries, feel free to contact us:
PerfettoLab of Bioinformatics, University of Rome "La Sapienza"
Head of the Lab: Dr. Livia Perfetto
Primary curator of MultiOmicsXplorer: Dr. Eleonora Meo
Email: eleonorameo.hp@gmail.com
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.