Data and Analysis from "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells"

Data, data processing and data analysis for manuscript "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells". (Preprint available here)

Analysis of AP-MS data: analysis.zip

Contains the following scripts as well as their outputs:

• 01_preparation.R R script for filtering and processing our mass spec data.
• 02_diffbinding.R R script for differential analysis followed by gene set enrichment.
• 03_funcstats.R R script for statistical analysis over different ontology terms.
• 04_semantic_analysis.R R script for the GO semantic analysis for the output of 02 and 03.
• 05_1_random_walks.py Python script for performing random walks for specific functional terms.
• 05_2_random_walks_analysis.R R script for the analysis and visualization of the output of 05_1.

The required input data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) entry.

Interactive visualization of the results of most of this analysis is available on GitHub as a Shiny app.

Analysis of whole cell lysate: analysis_wholecelllysate.zip

Contains the following script, as well as its output:

• 01_analysis.R R script for loading the data and extracting/visualizing KRAS and effector abundances.

The required data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) entry.