Extracellular proximal interaction profiling by cell surface-targeted TurboID reveals LDLR as a partner of liganded EGFR

Al Mismar et al. developed extracellular TurboID (ecTurboID) a method optimized for use on the cell surface. The authors used it to identify the extracellular interactomes of several transmembrane proteins and ligand-dependent changes in the interaction partners of the epidermal growth factor receptor (EGFR) and the the low-density lipoprotein receptor (LDLR). This study contains Gene Ontology (GO) enrichment dot plots.

Data and results description

GO enrichment analysis was performed in g:Profiler using default parameters and the human database. Data were downloaded as .xlsx files, with the adjusted p-value (g:Profiler default g:SCS) and number of genes in each GO term included. Enrichment dot plots were generated using GO Terms Dot Plot Visualizer Tool (https://github.com/gingraslab/go_terms_dot_plot) that visualizes the top enriched GO terms of gene lists from different baits or conditions (the top five terms for each category assessed were plotted in this paper). In GO enrichment dot plots, the color of the circle refers to the adjusted p-value of enrichment generated by g:Profiler and the size of the circle refers to the number of preys (genes) in the dataset contributing to the term’s enrichment.

Code instructions

The complete instruction can be found on: https://github.com/gingraslab/go_terms_dot_plot

Running the Tool

First you need to clone repository:

git clone https://github.com/gingraslab/ecTurboID_reprodicibility

To run the tool, navigate to the main directory in your terminal and execute the following command:

python3 go_terms_dot_plot.py

The tool will prompt you to enter:

1. The directory containing the input Excel files.
2. The number of top terms you wish to extract based on 'p-value'.

Example:

(base) Admin@Desktop% python3 go_terms_dot_plot.py
Please enter the directory: data
Please enter the name of the GO file: hnRNPA1_BFDR1%.xlsx
Please enter the number of top rows to keep based on 'adjusted_p_value' (default is 15): 5
Please enter the term size cutoff (default is 500): 2500
Please enter 'True' for filled version or 'False' for unfilled version (default is True): True

The generated plots will be saved in the 'results' folder.

Input

The tool expects g:Profiler output in .xlsx format. Each condition should be represented in a separate sheet within the Excel file.

Output

The tool generates a dot plot with:

Top GO terms on the y-axis. Conditions on the x-axis. Size of dots representing the number of genes. Darker color representing higher significance.

Sample Files and Results

There are two sample input files in the 'data' directory for your reference. Sample results are available in the 'results' directory.