Additional file 1 of Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages

Additional file 1. Gene set enrichment analysis. The Excel file (.xls) shows the output of gene set enrichment analysis (GSEA) [49, 50] of pre-ranked gene lists from the rat LSEC and KC RNA-seq datasets, associated with Gene Ontology (GO) biological processes (BP). The genes were pre-ranked based on expression. We have used the C5 collection of annotated gene sets in the Molecular Signatures Database (release 6.2; BP) [53] which consists of gene sets derived from GO [51, 52]. Name of worksheets: “GSEA_plot”, “GSEA_RNAseq_LSEC_BP”, and “GSEA_RNAseq_KC_BP”. The worksheet named “GSEA_Plot” contains the selected enriched BPs shown in Fig. 4.

附加文件1：基因集富集分析。本Excel文件（.xls格式）展示了大鼠肝窦内皮细胞（Liver Sinusoidal Endothelial Cells, LSEC）与库普弗细胞（Kupffer Cells, KC）RNA测序（RNA-seq）数据集的预排序基因列表的基因集富集分析（Gene Set Enrichment Analysis, GSEA）[49, 50]结果，该分析关联基因本体（Gene Ontology, GO）生物过程（Biological Processes, BP）术语。基因依据表达量完成预排序，本研究使用了分子特征数据库（Molecular Signatures Database，版本6.2；BP子集）[53]中的C5注释基因集集合，该集合的基因集均源自基因本体（GO）[51, 52]。工作表名称依次为“GSEA_plot”、“GSEA_RNAseq_LSEC_BP”以及“GSEA_RNAseq_KC_BP”。名为“GSEA_Plot”的工作表包含了图4中展示的筛选得到的富集生物过程条目。