A Dashboard for the Visualisation of a Protein’s PTMs

Simon Hackl, Theresa Harbig, Caroline Jachmann, Mathias Witte Paz, Kay Nieselt

View presentation:2022-10-16T20:10:00ZGMT-0600Change your timezone on the schedule page
2022-10-16T20:10:00Z
Exemplar figure, described by caption below
The proposed visualization of the PTMs applied to the human ALDOA protein. It consists of two main components: a contact map and a presence-absence heat map. The contact map shows the residues of close proximity (at most 6 Angstrom) where color encodes how many PTMS two residues in contact share. The presence-absence heat map shows the PTM composition of the protein along the primary sequence. Finally, we have included bar charts to summarise the number of PTMs by positions and single-axis traces that visually encode the secondary structure of each residue. All these components are part of an interactive dashboard.

The live footage of the talk, including the Q&A, can be viewed on the session page, Bio+MedVis: Challenges.

Abstract

In our submission we address the redesign task of the Bio+MedVis Challenge 2022. The existing visualization shows all post-translational modifications (PTMs) identified on a protein as circles that are connected to their position on the protein’s primary sequence by a line. Overall, the figure communicates well that there can be significantly more PTMs on proteins than anticipated. However, the visualization suffers from overplotting in multiple dimensions, rendering a detailed interpretation impossible. First, on the x-axis adjacent positions may carry PTMs, which causes the circles to overlap. Second, on the y-axis the PTMs for a position are stacked. From the visualizations, it is not clear if some PTMs are not displayed due to space limitations. Moreover, there are more different PTMs than there are colors that can be differentiated and a legend is missing. Most importantly, the visualization is based only on the primary sequence. No (visual) relation between PTMs and the protein structure can be established.