RRHO2-Analysis-of-Differential-Gene-Expression

Overview

This project performs Rank-Rank Hypergeometric Overlap (RRHO2) analysis on gene expression data to compare wild-type (WT) and HuR knockout (KO) conditions. The analysis helps visualize gene expression similarities and differences between the two datasets.

Project Structure

RRHO2_analysis/
│-- WT_E20_vs_WT_DMSO_deseq2.xls            # Wild-type gene expression ranking
│-- HuRKO_E20_vs_HuRKO_DMSO_deseq2.xls      # HuR knockout gene expression ranking
│-- RRHO2_wt_HuR.tiff                       # Output heatmap image
│-- RRHO2_analysis.Rmd                      # RMarkdown script for analysis

Requirements

Ensure you have the following R packages installed:

install.packages(c("dplyr", "ggplot2", "grid", "readxl","tidyverse", "devtools"))
# Install RRHO2 separately
devtools::install_github("yah2012/RRHO2")

Data

Place the following files in the working directory:

• wt_treatment_effect_deseq2_annotated.xls
• abi1_treatment_effect_deseq2_annotated.xls

Usage

Run the analysis using the provided RMarkdown (.Rmd) file:

1. Open analysis.Rmd
2. Execute code chunks or knit to an HTML report

Alternatively, run it as a standalone R script:

rmarkdown::render("analysis.Rmd")

Expected Output

• Venn Diagram & Heatmap: Visualizing overlap between WT and ABI1.
• Summary Statistics: Gene overlap and correlation analysis.
• TIFF Image: RRHO2_wt_HuR.tiff (for publication-ready visuals).

Contact

For questions or issues, feel free to open an issue on GitHub.