In this study, we aimed to develop a genetic signature for systemic lupus erythematosus (SLE) diagnosis through bioinformatic analyses of whole blood transcriptome data.Fourteen whole blood transcriptome datasets with at least 20 patients with SLE and 10 controls were integrated with RRA, which included GSE110685, GSE112087, GSE99967, GSE110169, GSE88884, GSE65391, GSE72509, GSE45291, GSE49454, GSE61635,GSE50635, GSE39088, GSE20864 and GSE17755.RRA outcomes suggested that most of those top 100 DEGs were from type I interferon-related pathways such as IFI44L, IFI27 and IFIT1. The top 10 upregulated genes included IFI44L, IFI27, RSAD2, IFIT1, HERC5, IFIT3, IFI44, OASL, CMPK2 and USP18 and were all from type I interferon-related pathways, which were preliminarily selected as one SLE diagnostic genetic signature referred to as RRAtop10 in this study.Based on the gene co-expression modules calculated above, a more complex gene signature was developed by selecting at most 10 genes from each upregulated co-expression module.This complex gene signature (referred to as RRAWGCNA10) consisted of 34 key genes from six independent co-expression modules and included IFI44L, IFI27, RSAD2, IFIT1, HERC5, IFIT3, IFI44, OASL, CMPK2, USP18, LHFPL2, RRM2, CEACAM6, CEACAM8, DEFA4, HP, LCN2, MMP8, OLFM4, OLR1, RNASE2, TCN1, ANKRD22, CASP5, CEACAM1, CLEC4D, DHRS9, DYNLT1, FCGR1B, TLR5, TNFAIP6, TNFSF13B, ANXA3 and SLC26A8.Among those 34 genes, the first 10 genes were identical to those genes in RRAtop10 and were all from the same co-expression module.In summary, this study developed useful gene signatures for SLE diagnosis through bioinformatic analyses of whole blood transcriptomic data, which could effectively differentiate SLE in different datasets and may provide some assistance in the classification of SLE.