Interactive Dataset from R2HaPpY EGF Stimulation Timecourse

Welcome to the Interactive Dataset

This Shiny app enables in depth queries of the largest phosphotyrosine (pY) dataset of EGF stimulation timecourse to date from BioRxiv/R2HaPpY.

TAB1 Search full dataset for your favorite protein(s).

TAB2 & TAB3 Interrogate the heatmap of 878 regulated pY sites.

TAB4 Perform gene ontology enrichment analysis of heatmap selection.

Note: Sites/Isoforms queried on Tab 1 - Boxplots of all data contain both unchanging and statistically changing sites. TABs 2-4 focus on only statistically changing sites.

Important: Be sure to brush heatmap rows or enter keywords on Tab 2 - Interactive Heatmap to feed input for TABs 2-4.

Read the pre-print at BioRxiv/R2HaPpY.

Figure 1: Preprint

Want to generate your own data? Visit full protocol at protocols.io.

Figure 2: Screenshot of Protocol

Resources

Need Help? Contact the developer (alexisn1@uw.edu) or GitHub alexis-cmyk.

Want to generate your own data? Read at BioRxiv/R2HaPpY and at protocols.io.

Like the heatmap? Contact the developer Zuguang Gu aka JokerGoo on GitHub JokerGoo.

Citations

Chang, A., Rodriguez-Mias, R., Berg, M. Moggridge, S., Villen, J. (2025). R2HaPpY: Rapid, robotic phosphotyrosine peptide enrichment using HaloTag-Src SH2 pY superbinder. bioRxiv. https://www.biorxiv.org/content/10.1101/2025.05.14.653984v1

Gu, Z. & Huebschmann, D. (2021). Make Interactive Complex Heatmaps in R. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab806

Kolberg, L., Raudvere, U., Kuzmin, I., Vilo, J., & Peterson, H. (2020). gprofiler2-an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Research. R package version 0.2.3.

In this tab, explore phosphosite/isoform intensities from tyrosine-specific and global phosphopeptide enrichments of EGF stimulation timecourse in HeLa cells.

Tips:

You may search multiple proteins/genes simultaneously. To do so, separate terms by vertical bar '|' in regex, or by comma in manual input

Hover over plot for additional protein information.

Regex and Manual input searches query all proteins assigned to a phosphosite. Ambiguous gene/protein identifications are indicated upon plot hover.

Check different dataset types. Proteins may not have phosphosites found in both tyrosine-specific and global phosphopeptide enrichment.

Click to expand for 'How To Example'

Boxplots of all data queried by regular expression, keyword or drop-down menu

Use 'Gene Input Priority' radio buttons to select query mode ('Regex Search', 'Dropdown Selection', 'Manual Input', 'Reference Gene')
Select type of data to display: 'pY SITE', 'pY ISOFORM', 'GLOBAL SITE', and 'GLOBAL ISOFORM'. Global refers to global phosphopeptide enrichment while pY is from R2HaPpY
Enter query in associated field. For 'Regex Search', partial names can be entered. Separate search terms with vertical bar.

Currently, 'Regex Search' is the only search format to query synonymous gene names and additional proteins from ambiguous peptide assignment when applicable.

In contraxt, 'Manual Input' requires full gene_site or gene_isoform search terms, separated by ',' commas.
Hover over plot area to see alternative gene names and ambiguous protein assignment info when applicable.
Plots populate automatically, 12 per page. Use Pagination field at top of sidebar to advance pages. Note, arrows appear upon hovering over page field. Green tip box indicates total genes, sites and pages returned in a query.
Use sliders to modify plot height, width, text size of panel title (strip text size), number of rows and columns in layout.
Save the displayed plot page using format dropdown and 'Save Boxplot' button at bottom of sidebar.

See below for screenshot example of how to do this.

Example of pY site selection

Use this tab to format and save heatmap subheatmap selection from TAB2

Click to expand for 'How To Example'

Format-friendly Subheatmap:

Displays the heatmap of brushed sites or Regular Expression Keywords input from the previous tab.
Customize size and font, then download a publication-ready PNG or PDF.

Example:

Use this tab to explore gene ontology enrichments for heatmap selections from TAB2.

Click to expand for 'How To Examples'

GO Enrichment:

Run enrichment on brushed genes (from heatmap) using gprofiler2.
Choose background gene set: Full Human Proteome or only genes identified in this study.

Default background set is full human proteome.

Adjust GO term type, correction method, and plot size.
Press 'Run/Update'.
Results present in graphical and tabular format. Reorder columns by clicking column title. Scroll down for pagination controls.
Reorder columns by clicking column title. Scroll down for pagination controls.