Fig. 2

Genes associated with oxidative phosphorylation (mitochondria function). a Enrichment plot of KEGG_Oxidative phosphorylation gene set identified by GSEA. Middle section (black bars) illustrate the position of the genes belonging to the gene set in the context of all the genes on the Affymetrix U133 plus 2.0 array. The enrichment score (ES) plotted as a function of the position within the ranked list of array genes is shown as a green line. The ranked list metric shown in gray illustrates the correlation between the signal to noise values of all individually ranked genes according to the neutrophil samples of the ‘before’ and ‘after’ tocilizumab treatment (experimental conditions). b on the left is GSEA-derived heat map of the 110 leading edge genes that correlates with response to tocilizumab and contributing to the enrichment score; on the right is the top 20 genes that includes some of the genes mapped by IPA to mitochondria dysfunction pathway (in red asterisks). Signal intensities are illustrated by varying shades of red (increased) and blue (decreased). c Quantitative real-time polymerase chain reaction (qRT-PCR) validation of differentially expressed genes (NDUFB2, COX6C, LAT) observed in this microarray experiment. The relative fold change of both microarray (solid bar) and qRT-PCR (open bars) are shown. The data for qRT-PCR are the average of 3 independent experiments done on the same sample