Transcription factor–gene regulatory network (TF-GRN) matrix, TF ChIP-seq data, TF ChIP-seq metadata and supplementary data (Data S1–S9) for CATaN

Abstract This record provides the input datasets for CATaN, comprising a transcription factor–gene regulatory network (TF-GRN) matrix and the underlying transcription factor (TF) ChIP-seq resources. The TF-GRN matrix was derived from a large TF ChIP-seq compendium comprising 2,868 profiles covering 410 TFs across 24 tissues and 287 cell types. All genomic coordinates are based on the human reference genome hg19. In addition, this record includes supplementary data tables (Data S1–S9) reporting the results of applying CATaN to seven datasets. Files TF_GRN_matrix.txt — TF-GRN matrix. A matrix of TF–gene connectivity scores, where rows correspond to genes and columns correspond to individual TF ChIP-seq samples. TF_ChIPseq_bed_hg19.tar.gz — TF ChIP-seq peak regions. An archive containing 3,158 BED files (including 2,868 TF ChIP-seq samples used for the TF-GRN matrix), each representing the ChIP-seq peak regions of one TF profile (hg19). Files are named using the convention <GEOid>_<TFpname>.hg19.bed. TF_ChIPseq.info — TF ChIP-seq metadata. A table describing each ChIP-seq sample, with the following columns: TF protein name (TFpname), TF gene name (TFgname), GEO sample ID (GEOid), tissue of origin (Cell), and cell type (Cell_CA). CATaN_SupTable_DataS1_9.xlsx — Supplementary data (Data S1–S9). An Excel workbook containing the results of applying CATaN to seven datasets, presented as nine data tables (Data S1–S9). The rheumatoid arthritis (RA) synovium dataset is presented as three tables (all cell types, and the T cell and B cell subsets), while each of the other six datasets corresponds to a single table. Each data table comprises four components: transcriptome sample loadings (A), TF sample loadings (B), transcriptome gene projections (C), and stratified LD score regression (S-LDSC) results for the CC annotations (D).