Network Analysis

The genes mentioned before which were significantly changed the most in malaria patient were put in GeneMANIA, a program in which the physical

 

-> Experimental group VS Baseline group (green lines are the gene interaction between the genes).

 

 

-> treated VS acute Malaria groups (green lines are the gene interactions and the red lines are the physical interaction between the genes).

 

 

 

Important genes

Treated VS Acute malaria: Sinificantly changed genes with the highest (lowest) logFC

ENS_ID	LogFC	FC	Avr_exp	T	external_gene_ID	Description
ENSG00000204388	-2,84	-7,17	6,11	-3,54	HSPA1B	Heat shock 70kkDa 1B
ENSG00000204389	-2,20	-4,61	8,43	-3,99	HSPA1B	Heat shock 70kDa protein 1B
ENSG00000147872	-2,17	-4,49	8,17	-3,96	PLIN2	Perilipin 2
ENSG00000148926	-1,28	-2,43	4,49	-2,61	ADM	Adrenomedullin
ENSG00000103569	-1,38	-2,60	6,91	-3,10	AQP9	Aquaporin 9

Looking at the post which was send before, the Adrenomedullin genes seems to appear in both the experiment. Futher reaserch for this gene should be done for knowing its effect (role) in malaria.

Important significant changed genes

Experimental VS Basline: Table with genes that were significantly change wiith the highest FC.

ENS.ID	logFC	FC	AveExpr	t	External_gene_ID	Description
ENSG00000169245	4,23	18,79	5,26	10,97	CXCL10	Chemokine ligand 10
ENSG00000117228	4,20	18,33	7,18	19,96	GBP1	Guanylate binding protein 1, interferon-inducible
ENSG00000140105	4,04	16,50	7,59	21,58	WARS	Tryptophanyl-tRNA synthase
ENSG00000149131	3,96	15,55	4,24	15,20	SERPING1	Serpin peptidase inhibitor
ENSG00000002549	3,68	12,86	7,48	17,06	LAP3	Leucine aminopeptidase 3
ENSG00000130489	3,25	9,53	6,11	13,25	SCO2	SCO2 cytochrome c oxidase assembly protein
ENSG00000151726	3,23	9,42	6,41	11,30	ACSL1	Acyl-CoA synthase long-chain family member 1
ENSG00000137959	3,12	8,70	5,21	7,32	IFI44L	Interferon-induced protein 44-like
ENSG00000168899	3,10	8,60	5,48	13,90	VAMP5	Vesicle-associated membrane protein 5
ENSG00000187608	2,87	7,30	7,46	10,88	ISG15	ISG15 ubiquitin-like modifier
ENSG00000148926	2,11	4,31	3,84	6,75	ADM	Adrenomedullin
ENSG00000135604	2,02	4,06	4,28	8,53	STX11	Syntaxin 11
ENSG00000157601	2,31	4,95	6,00	7,27	MX1	Myxovirus (influenza virus) resistance 1, interferon inducible protein p78 (mouse)

Week 5&6

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

 

 

Table group experimental VS baseline_ genes with the lowest logFC

 

Tab;e group experimental VS baseline_genes with the highest log FC

 

Table group experimental VS baseline_genes with the moest significantly p-value