发表在NATURE COMMUNICATIONS | (2021) 的 文章:《CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells》,链接是:https://www./articles/s41467-021-26091-4 就做了差异分析:
最开始是 13,433 PB and 12,239 TI cells,整体来进行降维聚类分群后,根据 FOXP3 and CD25 (IL2RA) 定位到Treg亚群, 分别是 160 PB and 574 TI Treg cells
如果是这两个分组做差异分析,273 differentially-expressed genes (DEGs) (Log fold-change > 1, adjusted p-value < 0.05) by comparing TI versus PB Treg cells.
a Trajectory manifold of Treg cells from the ccRCC using the Monocle 2 algorithm. Solid and dotted lines represent distinct cell trajectories/fates defined by expression profiles.
my_cds_subset=cds # pseudotime is now a column in the phenotypic data as well as the cell state head(pData(my_cds_subset)) # 这个differentialGeneTest会比较耗费时间 my_pseudotime_de <- differentialGeneTest(my_cds_subset, fullModelFormulaStr = "~sm.ns(Pseudotime)", cores = 1) # 不知道为什么无法开启并行计算了
b Pseudotime projections of transcriptional changes in immune genes based on the manifold. The significance was determined based on differential testing relative to the site of origin which was also used to generate pseudotime and adjusted for multiple comparisons.
热图里面的基因其实有 多种展现方式:
c Expression heatmap of significant (q < 1e-6) genes based on branch expression analysis comparing the two TI cell fates. The genes in the heatmap were also used in the ordering of the pseudotime variable.
以及:
d Cell trajectory projections of transcriptional changes in immune genes based on the manifold. Significance based on differential testing between the first and second cell fates of TI Treg cells. "x denotes the scaled mean mRNA levels at each pole of the manifold.