In this week I took a look at the pathways and I did not find anything special to mention. Also there were not enough genes that followed the criterion from ( [logFC] < -0.585 OR [logFC] > 0.585) AND [P.Value] < 0.0 so I change it in ( [logFC] < -0.263 OR [logFC] > 0.263) AND [P.Value] < 0.0
The folowing tables represend the ranking with the new mentioned criterion.
Z-score Experimental VS baseline
Z-score Acute VS treated
The positive gene that followed the criterion rose, and also the ranking differs from the previous criterion (these tables are shown in the previous blog
More inflamation pathways are shown like Nf-kb, IL pathways, toll like receptors pathways
Quercetin and Nf-Kb/AP-1 induced cell appoptosis. The highest ranked pathway in the acute treated group.
It is expected that afther treatment genes in inflamation pathway will be downregulated. So I wanted to take a look at gene with an high (low) FC and a significant p-value, that were not found in pathvisio.
--> TREATED VS ACUUT
Table group acuut VS treated_genes with the lowest logFC
Table group acuut VS treated_genes with the highest logFC
Table group acuut VS treated_genes with the lowest p-value
--> EXPERIMENTAL VS BASELINE