By comparison of the transcriptome profiles of udder quarters neighboring to infected quarters and healthy udder tissue we analyse gene expression in the late stage of infection with E. coli 1303. Differentially expressed genes and transcription factors regulating coexpressed genes identified by SOTA clustering were used to identify key genes that define systemic reactions to infection with E. coli 1303. Keywords: disease state analysis Overall design: 10 samples, two conditions: udder quarters neighboring to one which was treated with E. coli for 24h vs healthy control * five replicates