2026-10-13T16:01:54Z https://www.scidb.cn/oai

10.57760/sciencedb.011ri 2026-09-09T15:21:57Z

2026-09-09 Re-annotation of a fixed platelet-activation gene set to its stromal sources in gastric cancer: reproducible analysis code and result tables doi:10.57760/sciencedb.011ri en This dataset is the fully reproducible computational archive of a bioinformatic study of the gastric cancer tumor microenvironment. It re-annotates a set of genes originally annotated by circulating-platelet-activation function (platelet-activation-annotated genes, PAG) to their actual cellular sources within gastric tumors, and quantifies how the resulting program relates to cancer-associated fibroblast (CAF) states and to the spatial distribution of CD8 T cells.The archive contains 37 R scripts organized into six ordered stages (bulk prognostic modeling, discovery single-cell cohort, spatial transcriptomics, independent single-cell replication, immunotherapy cohort, and reviewer robustness analyses); a frozen 11-gene LASSO-Cox coefficient table that is only loaded and never re-estimated downstream; four small input tables; 105 author-run result CSVs that serve as a table-by-table numerical reference; a dependency-check script; an English README with data access, directory layout, run order, random seeds and interpretive boundaries; and an MIT license.Analyses use public data: TCGA-STAD, GEO GSE84437/GSE15459/GSE183904/GSE150290/GSE251950, and ENA PRJEB25780. Raw reads and large expression matrices are not included and must be obtained from these repositories following the README; the workflow reproduces all statistics and figures from the processed inputs. The global random seed is fixed at 2026 (42 for AUCell; 1000 CellChat permutations) and the reference environment is R 4.6.1. The archive supports result verification, method reuse, and follow-up work on stromal immune exclusion in gastric cancer. gastric cancer; tumor microenvironment; cancer-associated fibroblasts; single-cell RNA sequencing; spatial transcriptomics; immune exclusion rz z EMBARGO https://creativecommons.org/licenses/by-nc-nd/4.0/ dataset Science Data Bank