Functional Investigation

To further help with the investigation of the clusters found we have implemented several post cluster functions. These are plugins to WebgestaltR WebgestaltR on Cran and to do a string analysis of the genes STRINGdb.

GenesPerGeneSet

Checking out which genes are in which cluster can be done with GenesPerGeneSet.

IPA.KOvsWT.genes <- GenesPerGeneSet(IPA.KOvsWT)
View(IPA.KOvsWT.genes)

Genes Per GeneSet

If we have enough genes per cluster its possible to investigate these clusters furhter. This can be done with the unique genes per cluster and all the genes in the cluster. If there are only a few unique genes in a cluster its not advised to analyze the unique genes.

ORA via WebgestaltR


require(WebGestaltR)
IPA.KOvsWT.ORA.all <- ORAGeneSets(Object = IPA.KOvsWT, ORA.returned = 10, unique.per.cluster = F)

View(IPA.KOvsWT.ORA.all)

STRINGdb

There is also the STRINGdb plugin, which due to the functioning of the STRINGdb package is 2 seperate functions.


IPA.KOvsWT.String.all <- GetSTRINGdbPerGeneSets(Object = IPA.KOvsWT, unique.per.cluster = F)

par(mfrow=c(2,3))
for(i in 1:6)
{
  plotSTRINGdbPerGeneSets(StringObject = IPA.KOvsWT.String.all, plot.cluster = i)
  plotSTRINGdbPerGeneSets(StringObject = IPA.KOvsWT.String.all, plot.cluster = i)
  plotSTRINGdbPerGeneSets(StringObject = IPA.KOvsWT.String.all, plot.cluster = i)
  plotSTRINGdbPerGeneSets(StringObject = IPA.KOvsWT.String.all, plot.cluster = i)
  plotSTRINGdbPerGeneSets(StringObject = IPA.KOvsWT.String.all, plot.cluster = i)
  plotSTRINGdbPerGeneSets(StringObject = IPA.KOvsWT.String.all, plot.cluster = i)
  
}

STRING