Overrepresentation test of differentially expressed genes from GATA3+ Th2 cell-specific clusters

Published: 31 March 2023| Version 1 | DOI: 10.17632/t9wc5vznwy.1
Wilson Jr Aala,
, Maria Papanikolaou, Natashia Benzian-Olsson, Alexandros Onoufriadis, Hans I-Chen Harn,
, Kurt Lu, John McGrath,


PANTHER ORA of GATA3+ Th2 cells (Cluster 3 and Cluster 0) using Fisher's exact test on Biological Process annotation dataset and FDR method for multiple testing p-value adjustment. Differentially expressed genes were obtained by using FindAllMarkers function of Seurat on the T cell subset of the integrated single cell RNA sequencing dataset of affected and unaffected dominant dystrophic epidermolysis bullosa and healthy skin. Cluster-specific DEGs were obtained by first annotating each DEG for cluster occurrences using a custom R script, and subsequently filtering genes that have expression on other clusters. Besides enrichment for T cell-related pathways, multiple glycolysis-related terms are enriched only in Cluster 3.



National Cheng Kung University