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)用于运行Incytr的输入数据，源自《基于多模态数据的细胞信号通路发现》（Cell signaling pathways discovery from multi-modal data）一文所述： mc38_input_data: pr_10、pr_14：分别对应10天与14天培养条件下经细胞类型反卷积得到的总蛋白质组学数据 ps_10、ps_14：分别对应10天与14天培养条件下经细胞类型反卷积得到的pS磷酸化蛋白质组学数据 py_10、py_14：分别对应10天与14天培养条件下经细胞类型反卷积得到的pY磷酸化蛋白质组学数据 kldata：针对观测到的磷酸化位点的激酶文库（Kinase Library）预测结果 mc38b.rds：包含单细胞RNA测序（scRNA-seq）数据的Seurat对象（Seurat object） input_gene_list：转录组学数据中的标记基因与高表达基因 5xfad_input_data: processed_pr_5X_v2、processed_pr_WT_v2：分别对应5X模型组与野生型（WT）组条件下经细胞类型反卷积得到的总蛋白质组学数据 processed_ps_5X_v2、processed_ps_WT_v2：分别对应5X模型组与野生型（WT）组条件下经细胞类型反卷积得到的pS磷酸化蛋白质组学数据 processed_py_5X_v2、processed_py_WT_v2：分别对应5X模型组与野生型（WT）组条件下经细胞类型反卷积得到的pY磷酸化蛋白质组学数据 kldata：针对观测到的磷酸化位点的激酶文库预测结果 转录组学数据源自Zhou等人2020年的研究成果 covid_input_data: covid_bl_t_2024.rds：包含单细胞RNA测序（scRNA-seq）数据的Seurat对象（来自BL组的T细胞） additional_input_genes：除转录组学数据中筛选的高表达基因外，额外用于输入至Incytr模型的基因集 首批队列数据可于基因表达综合数据库（Gene Expression Omnibus, GEO）中获取，登录号为GSE186267