Data connected with "Cell signaling pathways discovery from multi-modal data"

Input data used to run Incytr as described in "Cell signaling pathways discovery from multi-modal data":

• mc38_input_data:
  • pr_10, pr_14: total proteomics for 10 and 14 day conditions deconvoluted by cell type
  • ps_10, ps_14: pS phosphoproteomics for 10 and 14 day conditions deconvoluted by cell type
  • py_10, py_14: pY phosphoproteomics for 10 and 14 day conditions deconvoluted by cell type
  • kldata: Kinase Library predictions for observed phosphosites
  • mc38b.rds: Seurat object with scRNA-seq data
  • input_gene_list: markers and highly expressed genes in transcriptomics data
• 5xfad_input_data:
  • processed_pr_5X_v2, processed_pr_WT_v2: total proteomics for 5X and WT conditions deconvoluted by cell type
  • processed_ps_5X_v2, processed_ps_WT_v2: pS phosphoproteomics for 5X and WT conditions deconvoluted by cell type
  • processed_py_5X_v2, processed_py_WT_v2: pY phosphoproteomics for 5X and WT conditions deconvoluted by cell type
  • kldata: Kinase Library predictions for observed phosphosites
  • transcriptomics is available from Zhou et al. (2020)
• covid_input_data:
  • covid_bl_t_2024.rds: Seurat object with scRNA-seq data (T cells from BL group)
  • additional_input_genes: additional genes used as input to Incytr besides those indicated through high expression in the transcriptomic data
  • First cohort data available at Gene Expression Omnibus (GSE186267)