Identification and functional analysis of differentially expressed genes

CJ Ciliang Jin
PJ Penglei Jiang
ZZ Zhaoru Zhang
YH Yingli Han
XW Xue Wen
LZ Lin Zheng
WK Wei Kuang
JL Jiangshan Lian
GY Guodong Yu
XQ Xinyue Qian
YR Yue Ren
ML Miaomiao Lu
LX Lingling Xu
WC Weixin Chen
JC Jiyang Chen
YZ Yuwei Zhou
JX Jinxia Xin
BW Ben Wang
XJ Xi Jin
PQ Pengxu Qian
YY Yida Yang
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Seurat function FindAllMarkers was used to find the cell type specific genes or differentially expressed genes between PBC and control samples with “logfc.threshold = 0.4, test.use = “MAST”” and “logfc.threshold = 0.3, test.use = “MAST”” respectively. The P values were adjusted by Bonferroni test. Most marker genes and differentially expressed genes are provided in Supplementary Data 2-10,11-17. For genes that may have a close relationship with the progression of PBC disease but have log-transformed fold changes less than 0.3, we have described the fold changes and adjusted P-values of these genes in the results section. R package clusterProfiler (v3.12) was applied to perform pathway enrichment analysis of given gene sets60.

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