SNO_proteomics

Differential Abundance of S-Nitrosylated Proteins and Functional Enrichment Analysis

This repository contains the R code and data analysis pipeline used to assess differential abundance of S-nitrosylated (SNO) proteins in human liver cancer cells. The analysis compares parental (HepG2) and Sorafenib-resistant (R-HepG2) cell lines, under treated and untreated conditions, followed by functional enrichment using KEGG pathways.

Overview

The main components of the analysis include:

• Data normalization using a class-specific quantile (CSQ) strategy to account for treatment and cell-type differences.
• Differential abundance analysis performed with the limma package on CSQ-normalized data.
• Over-representation analysis (ORA) of significantly changing proteins using KEGG pathway annotations.

Repository Contents

• SNO_proteomics.Rmd — R Markdown file containing the full analysis pipeline.
• SNO_proteomics.html — Rendered output of the Rmd file.
• SNO_proteomics.R — R script used to run the pipeline and generate figures and tables separately.
• functions_sno.R — Custom helper functions used in the analysis.
• SNO_proteomics.Rproj — RStudio project file for convenient setup.
• data/ — Folder containing input data (proteomics results, translation table).
• README.md — This description of the project and usage.

Reproducibility

This repository includes all code and data needed to reproduce the results shown in the manuscript. To replicate the analysis:

1. Open the RStudio project: SNO_proteomics.Rproj
2. Run or knit SNO_proteomics.Rmd to generate the full report.
3. Alternatively, source SNO_proteomics.R to generate figures and tables separately.

All required packages are installed/loaded in the Rmd file. A sessionInfo() is printed at the end for transparency on package versions.