v1.0.0

Discover insights from proteomics experiments with ease

Data Input
Reference Proteome:

Filter the samples

Select a variable to filter:

Identify Subgroup Differences

Investigate Subgroup Differences:

Analysis Options

Estimate variance across samples
Apply moderated t-test
Variable Stabilization:
Center the fold changes

Import/Export Config

Download Config

Welcome!

RokaiXplorer is an interactive tool designed for exploratory data analysis of proteomics and phospho-proteomics data to uncover novel biomarkers and potential clinical targets.

With RokaiXplorer, you can:

  • Identify significant changes in phosphorylation and protein expression with ease,
  • Perform enrichment analysis of gene ontology (GO) terms to gain insights,
  • Infer kinase activities using the RoKAI algorithm.
Need help getting started? Try our Interactive Tutorial!
Interested in exploring more? Learn about our Interactive Data Browser
Have questions or comments? Contact us or Leave Feedback

Thank you for using RokaiXplorer!

Contact

RokaiXplorer is designed by Serhan Yilmaz and Mehmet Koyuturk at Case Western Reserve University.
If you have any questions, please contact <serhan.yilmaz@case.edu>

Giving feedback

To make comments, suggestions or to report a problem, please use the form below:

References

Please check out the following manuscript for further information:
  • Yilmaz, S., Lopes, F. B. T. P., Schlatzer, D., Ayati, M., Chance, M. R., & Koyuturk, M. (2024) Making Proteomics Accessible: RokaiXplorer for interactive analysis of phospho-proteomic data. Bioinformatics Advances vbae077

In addition, the following resources are used in this application:
  • Yilmaz S., Ayati M., Schlatzer D., Cicek A. E., Chance M. R., Koyuturk M. (2021) Robust inference of kinase activity using functional networks Nature Communications 12 (1117)
  • Hornbeck, P. V. et al. (2015) Phosphositeplus, 2014: mutations, ptms and recalibrations. Nucleic acids research 43(D1), D512-D520
  • Licata, L. et al. (2020) SIGNOR 2.0, the SIGnaling network open resource 2.0: 2019 update. Nucleic acids research 48(D1), D504-D510
  • Minguez, P. et al. (2012) PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic acids research 41(D1), D306-D311
  • Szklarczyk, D. et al. (2014) STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic acids research 43(D1), D447-D452
  • Damle, N. P., & Köhn, M. (2019) The human DEPhOsphorylation Database DEPOD: 2019 update. Database

Dataset Versions

The versions (last modified dates) of the datasets used are as follows:

Share Your Data and Results Online with RokaiXplorer

Starting from v0.5.0, RokaiXplorer now allows you to easily share your datasets and analysis results online through an interactive data browser. Explore some examples below:

To deploy your own application, you will need:

  • The provided scripts from our Github page
  • R, RStudio, and Rtools (for Windows) installed on your system
  • Your data, metadata and expression data (if applicable) to be used in your application
  • An optional configuration file that can be generated from the Import/Export Config tab
  • A markdown .md file to display descriptions in the About section
  • A Shinyapps.io account to deploy your application online (which you can create for free)

For a detailed tutorial on deployment, please visit our Github page.

Click on a point to inspect it in detail.

Plot Options

Show Legend

Analysis Options

Apply FDR correction
Significant only
Plot Y-Axis:
Significant only
Show:
Double click on a row to inspect it in detail.

This network is interactive! You can drag & drop nodes to adjust the view and hover to see more information. Double click on a node to inspect it in detail.

Significant only
Single Kinases
Click on a point to inspect it in detail.

Plot Options

Show Legend

Analysis Options

Apply FDR correction
Significant only
Plot Y-Axis:
Significant only
Show:
Double click on a row to inspect it in detail.

This network is interactive! You can drag & drop nodes to adjust the view and hover to see more information. Double click on a node to inspect it in detail.

Significant only
Single Kinases
Click on a point to inspect it in detail.

Plot Options

Show Legend

Analysis Options

Apply FDR correction
Significant only
Plot Y-Axis:
Significant only
Show:
Double click on a row to inspect it in detail.
Click on a point to inspect it in detail.

Plot Options

Show Legend

Analysis Options

Kinase Substrate Dataset:
RoKAI Network:
Apply FDR correction
Significant only
Plot Y-Axis:
Significant only
Show:

Filtering Options

Double click on a row to inspect it in detail.
Double click on a row to inspect it in detail.

Inclusion Criteria (Enrichment Terms)

Include the following:
Filter by overlap

Number of terms:

Gene List for Enrichment

Datasource:
Apply FDR correction
Direction:

Number of proteins:

Click on a point to inspect it in detail.

Plot Options

Show Legend

Analysis Options

Statistical Test:
Apply Yates's correction
Enrichment Score:
Apply FDR correction

Filtering Options

Category:
Significant Only

Double click on a row to inspect it in detail.

Filtering Options

Category:
Significant Only
Show Hits Only

Double click on a row to inspect it in detail.
Data Source:
Report (Excel)
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