Fangji–Yiyiren–Fuling for rheumatoid arthritis: network pharmacology, public synovial transcriptomics and molecular docking data, code and reproducibility archive

This record provides the complete computational data, analysis code, results, figures, audit logs, manuscript files and supplementary materials supporting an integrative study of the Fangji–Yiyiren–Fuling herb combination (3:5:4) in rheumatoid arthritis (RA). RA is the sole disease scope of the study. Osteoarthritis samples present in the source GEO series were retained only as source data and excluded from all RA case-control contrasts. The workflow integrates network pharmacology; herb–compound–target curation; collection of RA-associated genes; STRING protein–protein interaction analysis; Gene Ontology and KEGG enrichment; discovery transcriptomic analysis using GSE55457; independent public-cohort validation using GSE55235; MCP-counter cell-population scoring; exploratory receiver operating characteristic analysis of hub genes; and AutoDock Vina molecular docking. The archive contains raw and processed data, reproducible analysis scripts, execution logs, result tables, eight main figures, manuscript and supplementary DOCX/XLSX files, 53 DOI-verified references with Crossref metadata, file manifests and SHA-256 checksums. Key outputs include 27 active herb–compound records, 353 unique predicted or curated drug targets, 2,377 RA-associated genes, 155 intersecting genes, 608 and 1,294 differentially expressed genes in the two GEO cohorts, 261 directionally concordant overlapping genes, ten prioritized hubs (EGFR, AKT1, HSP90AA1, HIF1A, STAT1, CASP3, JUN, BCL2, PIK3CA and PTGS2), and 50 completed compound–target docking pairs. All results are computational and hypothesis-generating. They do not establish clinical efficacy, direct target engagement or experimental binding and require prospective experimental validation.