BurnOmicsDB: a curated and standardized database of human burn injury transcriptomics across tissues, time points, and clinical contexts

Overview BurnOmicsDB version 1.0.0 is a curated, standardized, and gene-centered resource integrating human burn injury transcriptomic evidence across tissues, post-injury time points, wound stages, and clinical interventions. The resource is designed to enable clinicians and researchers without specialist bioinformatics training to search for a gene and rapidly examine its expression direction, effect size, and statistical evidence across multiple publicly available burn transcriptomic datasets. Database content This release integrates six human datasets from the NCBI Gene Expression Omnibus: GSE139028 GSE178411 GSE8056 GSE19743 GSE37069 GSE77791 Together, these datasets cover normal skin, burn eschar, burn wound margins, acute and late burn wounds, hypertrophic scars, peripheral blood, whole blood, longitudinal post-injury responses, healthy controls, and hydrocortisone-versus-placebo comparisons. BurnOmicsDB version 1.0.0 contains 22 predefined differential-expression contrasts and 448,735 gene–contrast result records. Each record represents one gene in one GEO dataset and one comparison. Data processing and standardization Each GEO dataset was processed independently using a platform-appropriate workflow for RNA sequencing or Affymetrix microarray data. Expression matrices from different datasets were not directly merged or subjected to cross-study batch correction. The database standardizes: NCBI Gene IDs, official gene symbols, Ensembl IDs, and gene names; tissue, sample context, time or disease stage; case and control definitions; direction of comparison; log2 fold change and fold change; nominal P values and false-discovery rates; differential-expression significance status; analysis, normalization, and annotation methods. Positive log2 fold-change values consistently indicate higher expression in the designated case group than in the designated control group. Gene search supports official gene symbols, aliases, NCBI Gene IDs, Ensembl Gene IDs, HGNC IDs, and full gene names using a human gene reference derived from the NCBI Homo_sapiens.gene_info resource. Important interpretation notes BurnOmicsDB reports results from bulk tissue and bulk blood transcriptomic measurements. Observed expression differences may reflect both intracellular transcriptional changes and differences in cell composition or tissue structure. Results from different GEO datasets should not automatically be interpreted as statistically independent replication. In particular, GSE19743 and GSE37069 contain substantially overlapping study cohorts. BurnOmicsDB is intended as a research and hypothesis-generation resource. It is not a diagnostic tool and should not be used as the sole basis for clinical decision-making. Data provenance and ethics This project is a secondary analysis of publicly available, de-identified human transcriptomic datasets. No new participants were recruited, and no new identifiable clinical data were collected. Persistent identifier DOI: 10.5281/zenodo.21648675