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 T-test), P-value, adjusted P-value 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 Curation-Tutorial (a gpml file).
In pathvisio I can created a visualization. I wanted to show the up- and down regulated geneexpression and the p-value.
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 [P-value]<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.
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Pathway | positive (r) | measured (n) | total | % | Z Score | p-value (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
ATF6-alpha | 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 |
miR-targeted genes in leukocytes -
TarBase | 6 | 108 | 128 | 5,56% | 3,11 | 0,006 |
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For the group where the experimental effected group is compared with the baseline group, the first then pathways that follows the criteria are shown.
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Pathway | positive (r) | measured (n) | total | % | Z Score | p-value (permuted) |
Type II interferon signaling (IFNG) | 5 | 35 | 38 | 14,29% | 10,4 | 0 |
RIG-I/MDA5 mediated induction of
IFN-alpha/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 toll-like receptor
signaling pathway | 4 | 120 | 152 | 3,33% | 3,85 | 0,004 |
Apoptosis | 3 | 80 | 85 | 3,75% | 3,62 | 0,009 |
Quercetin and Nf-kB/ AP-1 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 |
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***
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
z-score -- the z-score as computed by a fisher exact test on overrepresentation
p-value (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 p-value that is not founded by PathVisio
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