Project Synopsis: This repository explores the expression patterns of succinate dehydrogenase (SDH) genes in sarcomas, with a focus on SDHB. Our findings suggest that SDHB is overexpressed in undifferentiated pleomorphic sarcomas (UPS) and that its overexpression potentially correlates with worse survival outcomes.
This repository contains multiple files, including:
- R scripts for data processing, differential expression analysis, and visualization
- Documentation describing methods and results
- Supporting files for figures and tables
Two main cohorts were analyzed:
- IPO Cohort: Institutional data (DDLPS, LMS, and UPS sarcoma subtypes).
- Availability: The IPO data can be provided upon request (due to privacy/ethical considerations).
- TCGA-SARC Cohort: Publicly available data from The Cancer Genome Atlas for sarcoma (SARC) samples.
- DDLPS, LMS, and UPS subtypes were also analyzed in this cohort.
Key Findings:
- Overexpression of SDH genes (particularly SDHB) correlated with survival outcomes in the IPO cohort.
- Differential gene expression (DGE) analysis was confirmed in the TCGA-SARC cohort, supporting the role of SDH overexpression in sarcoma progression.
A variety of R packages were utilized for data manipulation, statistical analysis, and visualization:
-
Data Manipulation & Cleaning
dplyr,readxl,tidyr,tidyverse -
Differential Expression Analysis
limma,edgeR -
Survival Analysis
survival,survminer -
Visualization
EnhancedVolcano,ggplot2,ggpubr,ComplexHeatmap,gplots,forestploter,enrichplot -
Gene Set Enrichment & Pathway Analysis
GSEABase,fgsea,msigdbr,clusterProfiler -
Other Utilities
corto,rempsyc
(Depending on your specific R environment, you may need to install and load all of these packages to reproduce the analyses.)
- Clone the Repository
git clone https://github.com/YourUsername/Sarcoma-SDH.git