Aging transcriptome is Associated with Poor Outcome Post-Surgical Removal of Early-Stage Lung Cancer

This repository contains the analysis code used in our study of transcriptomic differences between younger and older patients with stage I lung adenocarcinoma (LUAD). The project focuses on lower-airway gene expression programs associated with age and prognosis after surgical resection.

Contents

Each cohort has a folder in which you wil find the following

• /scripts – R scripts for data preprocessing, differential expression, co-expression network analysis (MEGENA), and pathway enrichment.
• /counts – genes counts tables used for downstream anlaysis .
• /data – Metadata

Key Analyses

• Differential gene expression between younger vs. older patients and between recurrence vs. no recurrence among each age group.
• Identification of recurrence-associated transcriptional modules
• Pathway annotation and cross-cohort consistency checks (NYU, TCGA, TRACERx)

Requirements

• R (≥4.2) with packages: DESeq2, edgeR, MEGENA, ggplot2, ComplexHeatmap