The Selleckchem ONO-4538 genes of cluster 6 were first downregulated after 3 h and upregulated after 6 h. Metacore analysis of the genes from the individual clusters revealed a clear difference in functionality between the genes of cluster 2, 4, and 6. Genes from cluster 2 were involved in immune pathways, including the IL-17 and IL-1 signalling pathway (p value: 10−13 and 10−12, respectively) and the Toll-like receptor pathway (p value: 10−9). The genes that were downregulated at the latest time point (cluster 4) were part of several
cell cycle pathways, such as those involved in metaphase checkpoint control and APC-mediated cell cycle regulation (p value: 10−25 and 10−20, respectively). Genes from cluster 6 were involved in the cell cycle as well. The two most significant pathways were “start of DNA replication in early S phase” (p value: 10−6) and “the metaphase checkpoint” (p value: 10−6). Metacore analysis of genes from clusters 1, 3, and 5 did not result in significantly regulated pathways. Gene set enrichment analysis was used for the identification of gene sets affected by DON in order to unravel mechanisms of DON toxicity. This enables the comparison of our results with results already published in literature or derived from microarray studies. A three-step approach was followed. Torin 1 mw Firstly, GSEA was
performed on each of the nine treatment groups in relation to the control samples at the same time point. Up- and downregulation of significant gene sets were visualized in heat maps enabling comparison between the treatment groups. This resulted in 264 gene sets, obtained Inositol monophosphatase 1 from five gene set collections, that were significantly affected by at least one treatment. Secondly,
molecular concepts mapping was performed to further facilitate the biological interpretation. This provided a visualization of the overlap in genes among the significant gene sets from the combined gene set collections. Based on clusters of highly similar gene sets, the main biological events were elucidated. Molecular concepts mapping was performed for one treatment: 6-h exposure to 10 mg/kg. This treatment was selected since nearly all gene sets affected by any treatment were also affected by this dose at this time point. Thirdly, gene sets showing high overlap according to molecular concepts mapping were merged. The rationale for this step was that a high overlap is indicative for comparable biological effects. Heat maps were made to investigate the expression of the individual genes of merged gene sets for all treatment groups. The results of the molecular concepts mapping for all gene sets are shown in Supplementary Fig. 1. The gene sets upregulated by 6-h exposure to 10 mg/kg DON clustered into five themes: lymphocyte activation, inflammatory response, blood cell infiltration, late precursor T cells, and a combination of cell adhesion and cytoskeleton (Supplementary Fig. 1A).