CXCR4-associated immune network and metabolite binding in tubulointerstitial injury of diabetic nephropathy

This repository contains the complete R Markdown codes and bioinformatic scripts used in our study on Diabetic Nephropathy (DN) using human renal tubular tissue data. The repository consists of the following sequential scripts: # Included Scripts:- 01_GSE99325_pipeline.R:** R script for the initial preprocessing, background correction, and normalization of raw data from the GSE99325 dataset.- 02_GSE30529_pipeline.R:** R script for the initial preprocessing, background correction, and normalization of raw data from the GSE30529 dataset.- 03_Integrative_DE_DKD.Rmd:** R Markdown script covering cross-cohort dataset integration, quantile harmonization, batch effect removal via the ComBat algorithm, and Differential Expression Analysis (DEGs) using the limma package.- 04_Co-expression_network_analysis.Rmd:** R Markdown script executing the Weighted Gene Co-expression Network Analysis (WGCNA) pipeline, including variance filtering, soft-thresholding power (beta) evaluation, module generation, and clinical module-trait correlation. # Note on External Analyses:Downstream structural and network topology analyses including functional enrichment (clusterProfiler), PPI network extraction (STRING/Cytoscape), and molecular docking validation (AutoDock Vina for the CXCR4 receptor) were performed using specialized external software platforms as detailed in the methodology of the main manuscript.