Week 4 (14-18 May 2014)

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.

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
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 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    *** 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