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

Published: 31 March 2023| Version 1 | DOI: 10.17632/t9wc5vznwy.1
Contributors:
Wilson Jr Aala, Ping-Chen Hou, Yi-Kai Hong, Yu-Chen Lin, Yu-Rong Lee, Wei-ting Tu, Maria Papanikolaou, Natashia Benzian-Olsson, Alexandros Onoufriadis, Hans I-Chen Harn, Chen-Peng Chieh, Kurt Lu, John McGrath, Chao-Kai Hsu

Description

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.

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Institutions

  • National Cheng Kung University

Categories

Dermatology

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