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Background  Lipopolysaccharide (endotoxin, LPS) is a strong inducer of the innate immune response. It is widespread in our environment, e.g. in house dust and contributes to asthma. Compared to humans, horses are even more sensitive to LPS. However, data on LPS effects on the equine transcriptome are very limited. Using RNA-seq we analysed LPS-induced differences in the gene expression in equine peripheral blood mononuclear cells at the gene and gene-network level in two half-sib families and one group of unrelated horses.    Results  24 h-LPS challenge of equine immune cells resulted in substantial changes in the transcriptomic profile (1,265 differentially expressed genes) showing partial overlap with human data. One of the half-sib families showed a specific response different from the other two groups of horses. We also identified co-expressed gene modules that clearly differentiated 24 h-LPS- from non-stimulated samples. These modules consisted of 934 highly interconnected genes and included genes involved in the immune response (e.g.  IL6 ,  CCL22 ,  CXCL6, CXCL2 ), however, none of the top ten hub genes of the modules have been annotated as responsive to LPS in gene ontology.    Conclusions  Using weighted gene co-expression network analysis we identified ten co-expressed gene modules significantly regulated by  in vitro  stimulation with LPS. Apart from 47 genes (5%) all other genes highly interconnected within the most up- and down-regulated modules were also significantly differentially expressed (FDR < 0.05). The LPS-regulated module hub genes have not yet been described as having a role in the immune response to LPS (e.g.  VAT1  and  TTC25 ).    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3390-y) contains supplementary material, which is available to authorized users.

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells