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2.5. Differentially expressed genes (DEGs) and pathway enrichment analysis

SC Sini Cai
NY Ningbei Yin
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Default settings of the scanpy.tl.rank_genes_groups() function were used to identify differentially expressed genes (DEGs) based on Wilcoxon rank sum test results. Genes expressed in more than 10% cells and with |avg_logFC| values of >1 were considered to be differentially expressed; p_val_adj values of <0.05 were considered significant. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the clusterProfiler R package to evaluate the biological functions of cell‐type specific DEGs 16 ; p_val_adj values of <0.05 were considered significant.

Copyright and License information:  ©2024 The Author(s). Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.
This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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