Breast cancer–specific CIBERSORTx signature matrices (major, minor, subset levels) and associated reference resources

Title: Breast cancer–specific signature matrices and benchmarking datasets for digital cytometryVersion: 1.0Date: 2025-12-02Authors: [Toru Hanamura, Akinori Takase]Contact: [[e-mail]] --------------------------------------------------------------------------------Overview--------------------------------------------------------------------------------This repository contains all datasets generated to build and benchmark thebreast cancer–specific signature matrices described in the manuscript: "[A multi-resolution, breast cancer–optimized CIBERSORTx reference matrix rigorously validated using single-cell and bulk transcriptomes]" All data are provided as machine-readable, tab-delimited text files (.txt).No proprietary formats are used. Each file corresponds exactly to the dataused in the analyses presented in the manuscript and supplementary materials. These datasets include:1. Pseudo-bulk gene expression profiles2. Ground-truth cell-fraction used to generate the pseudo-bulk mixtures (from scRNA-seq)3. Pure-cell aggregated gene expression profiles (from scRNA-seq)4. Final signature matrices (major, minor, and subset resolutions)5. Reference profiles used for S-mode batch correction in CIBERSORTx6. Source gene-expression profiles used for B-mode batch correction in CIBERSORTx Each dataset is available at three annotation resolutions:- **major**- **minor**- **subset** The structure and content of each file type are documented below. --------------------------------------------------------------------------------File List and Descriptions-------------------------------------------------------------------------------- All files are tab-separated (.txt). ====================================1. PSEUDO-BULK DATA==================================== ### 1-1. Pseudo-bulk expression matrices These files contain gene-level pseudo-bulk expression profiles created byaggregating scRNA-seq data with known cell-type proportions. - pseudobulk_mixture_major.txt- pseudobulk_mixture_minor.txt- pseudobulk_mixture_subset.txt Columns: Samples Rows: Genes (HGNC symbols) Values: Normalized expression (non-log TPM) ### 1-2. Ground-truth cell fractions used to generate mixtures These matrices provide the true cellular composition of each pseudo-bulk sample. - pseudobulk_mixture_counts_major.txt- pseudobulk_mixture_counts_minor.txt- pseudobulk_mixture_counts_subset.txt Columns: annotation — Cell-type label (major/minor/subset level) cellcount — Number of single cells aggregated for the mixture name — Pseudo-bulk sample ID (e.g., att_00001) ====================================2. PURE-CELL AGGREGATED PROFILES==================================== These files contain aggregated gene expression profiles for each pure cell type(calculated by averaging all single-cell profiles belonging to each annotation). - pure_cell_major.txt- pure_cell_minor.txt- pure_cell_subset.txt Columns: Cell types Rows: Genes Values: Mean expression (non-log TPM) ====================================3. SIGNATURE MATRICES==================================== These are the final matrices used for digital cytometry. - signature_matrix_major.txt- signature_matrix_minor.txt- signature_matrix_subset.txt Columns: Cell types Rows: Selected marker genes Values: Gene expression used by CIBERSORTx ====================================4. S-MODE BATCH-CORRECTION REFERENCES==================================== Reference profiles used as input for CIBERSORTx S-mode correction. - single_cell_reference_matrix_major.txt- single_cell_reference_matrix_minor.txt- single_cell_reference_matrix_subset.txt ====================================5. SOURCE GENE-EXPRESSION PROFILES==================================== Gene-expression matrices used as source data before marker selection. - sourceGEP_major.txt- sourceGEP_minor.txt- sourceGEP_subset.txt --------------------------------------------------------------------------------How to cite-------------------------------------------------------------------------------- If you use these datasets, please cite the associated manuscript: [Full citation once accepted] For preprints, cite: [Preprint DOI] --------------------------------------------------------------------------------Data format and reproducibility notes-------------------------------------------------------------------------------- - All files are tab-delimited.- No missing values are present unless biologically inherent.- Gene identifiers follow HGNC symbols.- Samples and cell types use the exact labels consistent with the manuscript.- Signature matrices are fully compatible with CIBERSORTx (S-mode and B-mode). --------------------------------------------------------------------------------License-------------------------------------------------------------------------------- These datasets are released under the CC BY 4.0 license unless stated otherwise.Users are free to share and adapt the material with appropriate attribution. --------------------------------------------------------------------------------Contact-------------------------------------------------------------------------------- Department of Breast OncologyTokai University School of Medicine143 Shimokasuya, Isehara-shi, Kanagawa, 259-1193, JapanE.mail; [e-mail]