Fig. 3

Aberrant gene expression of SSc CD4+ T cells include inflammatory genes and relevant transcription factors. a Differentially expressed genes (DEGs) comparing RNA expression microarray data of CD4+ T cells isolated from SSc with HD, in which 1949 genes were downregulated (log₂FC < 0, FDR < 0.05) and 1980 genes were upregulated (log₂FC > 0, FDR < 0.05). b t-SNE clustering of identified DEGs in HD and SSc CD4 T cell samples. c GO analysis of down- and upregulated DEGs performed utilizing the DAVID online tool (https://david.ncifcrf.gov/). Bubble size refers to the size of GO term, and threshold represents the cutoff for statistical significance (p value < 0.05). Relevant GO terms are summarized in tables before the bubble plots. d TF enrichment analysis, utilizing the DoRothEA tool, of all interrogated genes ordered by normalized enrichment score (NES) of SSc compared to HD. Dotted red lines represent the cutoffs for statistical significance (NES < − 2 and p value < 0.01, NES > 2 and p value < 0.01). e Graphical representations of z-scores of genes relevant to T cell biology, including CD3E and IL2RA; transcription factors NFKB2, CTCF, EGR1, RELB, RUNX1, JUN, and FLI1; and DNA methylcytosine dioxygenase TET3