DDX55 Suppresses Enhancer and Promoter-like Transposable Elements to sustain naïve T cell homeostasis

Repository for the article: "DDX55 Suppresses Enhancer and Promoter-like Transposable Elements to Sustain Naïve T Cell Homeostasis" by Mengyue Wu et al. This repository contains all data and code associated with the analyses presented in the article. data.zip: includes the complete set of result files generated throughout the study. Files 01–09: provide the full analysis pipeline. Each file corresponds to a specific stage of the workflow, as detailed below: 01_Data_preprocess_analysis: Preprocessing of immune cell RNA-seq datasets and identification of naïve T cell type–specific genes for IRENTH.02_OntoVAE: Training of the OntoVAE model and in silico gene perturbation analysis.03_OntoVAE_results_analysis: Downstream analysis and visualization of OntoVAE outputs.04_Phenotype_association: Integration of GWAS and eQTL data to assess phenotype relevance.05_DDX55_aging_immune: Expression analysis of DDX55 across aging and immune disease datasets.06_Gene_DEA: Differential expression analysis of genes.07_TE_DEA: Differential expression analysis of transposable elements (TEs).08_Identification_of_enh_prt: Prediction and classification of TE loci with enhancer or promoter-like signatures.09_CutTagSeq_analysis: Analysis of Cut&Tag sequencing data.