At the end of the week I use one of the outcomming table that was also provide by R with the enssemble ID of all genes that were found and change pointed against the logFC, Fold Change, Average Expresssion, T value (outcome from the statistical Ttest), Pvalue, adjusted Pvalue and the B value for the analysis in PathVisio, this file has to put in for the import of the expression import.
In PathVisio I select the human gene database HS_Derby_20130701.bridge. I also import the wikipathways Homo sapiens CurationTutorial (a gpml file).
In pathvisio I can created a visualization. I wanted to show the up and down regulated geneexpression and the pvalue.
At last I did an statistical test for all the pathway. I wanted the pathways to be ranked following the criteria ([logFC]>0.585 OR [logFC]<0.585) AND [Pvalue]<0.05.
For the group where the treated group is compared with the group with acute malaria, the first then pathways that follows the criteria are shown.














Pathway  positive (r)  measured (n)  total  %  Z Score  pvalue (permuted) 
RB in Cancer  9  92  104  9,78%  6,02  0,001 
Neurotransmitter uptake and Metabolism In
Glial Cells  1  2  13  50,00%  5,28  0 
Transport of Glycerol from Adipocytes to
the Liver by Aquaporins  1  2  7  50,00%  5,28  0,003 
Activation of Chaperone Genes by
ATF6alpha  2  8  16  25,00%  5,1  0,005 
Signal amplification  2  11  56  18,18%  4,23  0,003 
Thrombin signalling through proteinase
activated receptors (PARs)  2  13  53  15,38%  3,82  0,005 
Activation of Matrix Metalloproteinases  2  15  66  13,33%  3,48  0,009 
Adipogenesis  7  122  132  5,74%  3,47  0,008 
FAS pathway and Stress induction of HSP
regulation  3  35  43  8,57%  3,15  0,022 
miRtargeted genes in leukocytes 
TarBase  6  108  128  5,56%  3,11  0,006 
























































For the group where the experimental effected group is compared with the baseline group, the first then pathways that follows the criteria are shown.







Pathway  positive (r)  measured (n)  total  %  Z Score  pvalue (permuted) 
Type II interferon signaling (IFNG)  5  35  38  14,29%  10,4  0 
RIGI/MDA5 mediated induction of
IFNalpha/beta pathways  4  48  181  8,33%  6,88  0 
Heme Biosynthesis  1  8  28  12,50%  4,31  0,013 
NOD pathway  2  30  43  6,67%  4,26  0,004 
Serotonin Transporter Activity  1  9  15  11,11%  4,04  0,027 
Interferon alpha/beta signaling  2  34  96  5,88%  3,95  0,017 
Regulation of tolllike receptor
signaling pathway  4  120  152  3,33%  3,85  0,004 
Apoptosis  3  80  85  3,75%  3,62  0,009 
Quercetin and NfkB/ AP1 induced cell
apoptosis  1  11  25  9,09%  3,61  0,03 
TAK1 activates NFkB by phosphorylation
and activation of IKKs complex  1  11  30  9,09%  3,61  0,035 




























***
positive (r)  the number of genes on the pathway that fulfill the criterion
meassured (n)  the number of genes on the pathway that have been measured in the data set
total  the total number of genes on the pathway
%  the percentage of measured genes that fulfill the criterion
zscore  the zscore as computed by a fisher exact test on overrepresentation
pvalue (permuted)  the change
Next week I planned to take a better look at these pathways, and compare these two groups (differences and comparisons), to try to link this with biological reasons.
And to take a look at the gene with a high FC and a significant pvalue that is not founded by PathVisio
















































