RUNX3 orchestrates a context specific transcriptional switch with opposite outcomes in gastric cancer metastasis

This repository contains the bioinformatics analysis code used in the study “RUNX3 orchestrates a context-specific transcriptional switch with opposite outcomes in gastric cancer metastasis.”
All scripts and pipelines are organized into four top-level folders:
• RNAseq_Code: RNA-seq downstream analysis code for metastatic gastric cancer cell lines HGC27 (p53-deficient/LOF), LMSU (TP53 R175H GOF), and NUGC4 (wild-type p53; ARF-defective), including analyses of TGFβ-stimulated conditions and inhibitor-perturbation datasets. The workflows cover differential expression (DESeq2-based), gene set/pathway analyses (e.g., GSEA/GO), EMT/apoptosis-related scoring, and figure-ready visualizations.
• ChIPseq_Code: ChIP-seq analysis code for HGC27 cells, including processing and downstream analyses of RUNX3 and chromatin-mark ChIP-seq datasets (e.g., peak calling, annotation, metagene/heatmap profiling, and motif/enrichment analyses) aligned to the human reference genome (GRCh38/hg38).
• TMA_Code: Code for tissue microarray (TMA) quantification and statistical analyses used in the manuscript, including nuclear scoring metrics (e.g., H-score/positivity) and figure generation for the two gastric cancer TMAs (ST8013b and ST810d).
• 74_liver_metastases_Code: Code used to analyze an independent institutional cohort of 74 resected gastric cancer liver metastases, including RUNX3 IHC intensity/positivity assessments and stratified analyses by histological differentiation grade.
This deposit provides analysis code (scripts/pipelines) used to generate the processed results and figure-level summaries reported in the manuscript. Raw sequencing data are described in the manuscript. For questions regarding the analysis code, please contact the corresponding author (Yoshiaki Ito; [e-mail]).