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
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Z-score Acute VS treated
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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.
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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
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Table group acuut VS treated_genes with the highest logFC
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Table group acuut VS treated_genes with the lowest p-value
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--> EXPERIMENTAL VS BASELINE
He Patricia, jammer dat je niet meteen iets ziet dat je zou verwachten en/of hopen.
BeantwoordenVerwijderenDat NFkB-signaling verlaagd is in de treated groep zou je inderdaad wel verwachten in humane macrofagen, en zoals ik het van hieruit kan beoordelen zie je dit inderdaad terug in de pathway. De TLR signaling pathway die tevens in de significant veranderde lijst van pathways staat bij acute vs treated, is die ook verlaagd qua inflammatie?
En wel interessant dat twee verschillende kanker-gerelateerde pathways terugkomen in dezelfde analyse. Zie je analogieen tussen deze twee of zijn het compleet verschillende genen die veranderd zijn?
Anyway, misschien is het een ideetje om me de .pgex file door te sturen, dan kunnen we makkelijker met je meekijken. Succes met je thesis in ieder geval!
Bart
Oh en over die quercetin-pathway:
BeantwoordenVerwijderenhttp://www.ncbi.nlm.nih.gov/pubmed/22215188
;)
Patricia, does the found fold change of those heat shock proteins match the fever malaria patients can suffer from?
BeantwoordenVerwijderen