Bioinformatics

GO analysis of memory DEGs was performed by DAVID v2021q4⁶¹ and ShinyGO v0.6.1⁶². GO analysis of memory DAR genes were performed by GREAT.

Functional protein association networks of mouse Themis2 and human THEMIS2 were constructed and KEGG Pathways of their networks were implemented by STRING⁶³.

Principal component analysis (PCA) of naïve Themis2^+/+ and Themis2^–/– Ly49H⁺ NK cells and memory Themis2^+/+ and Themis2^–/–NK cells was performed by using iDEP .96⁶⁴.

GSEA V4.2.3⁶⁵ was performed by using normalized expression in memory WT and Themis2^–/– NK cells and normalized enrichment score (NES) and FDR were computed.

For an integrative analysis of memory DEGs and memory H3K4me3 DARs, the absolute values of the log₂-transformed fold change of normalized expression of memory DEGs and the fold change of signal per million reads of memory H3K4me3 DARs were represented as scatter plots. Spearman’s correlation coefficients with their p values of all memory DEGs/ memory H3K4me3 DARs and these genes annotated with the GO term DNA-templated transcription were calculated by using cor.test() function in R (https://www.r-project.org/). A mouse gene list annotated with DNA-templated transcription was obtained by using biomaRt package in R.

The Venn diagram was drawn by Venny 2.0 (https://bioinfogp.cnb.csic.es/tools/venny/).

The knowledge-based network analysis on ZNF740 was performed by Ingenuity Pathway Analysis 20.0⁶⁶ and the protein-protein interactions in the nucleus were represented.