can I use cytoscape for genie3 result?
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17 months ago
Ali • 0

Hi

I wonder if i could use cytoscape for genie3(gene regulatory network) result for visualization of the interaction among the input genes.

regards


EDIT:

Thanks Leite

The result file was in the csv format, the major challenge for me was the selection of the best informative interaction (or the gene with highest number of interaction )as the file include 19k interaction when run cytoscape the interaction ////////////////////

This is the codes that I run. Is there any parameter that I should include

library(GENIE3)
library(igraph)
library(RCy3)
library(Rgraphviz)

expr_data <- as.matrix(read.table("upanddowngene.csv", header = T, sep = ",",row.names = 1))
set.seed(expr_data)

weightMat <- GENIE3(expr_data)
linkList <- getLinkList(weightMat)

edge_listsi <- linkList
Gsi <- graph.data.frame(edge_listsi,directed = F)
Asi <- get.adjacency(Gsi,sparse = F,attr = "weight",type = "both")

g_arasi <- graph.adjacency(Asi,mode = "undirected",weighted = T)
g.cyto <- igraph.to.graphNEL(g_arasi)

cw = createNetworkFromGraph("net", graph=g.cyto)
displayGraph (cw)

Regards

rna-seq RNA-Seq R • 818 views
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What is your genie3 output list ???? If it is a txt file with paired interacting genes and a value for each interaction, the answer is yes.

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@Ali

To process 19k interactions in cytoscape, you would have to have a super computer. Another point, your network would be unreadable.

You need to put a weight filter for interactions, then import into cytoscape.

Get only the links with a weight higher than some threshold

"Alternatively, a threshold can be set on the weights of the links:"

linkList <- getLinkList(weightMat, threshold=0.1)

I think you can get more information by reading this tutorial:

https://bioconductor.org/packages/devel/bioc/vignettes/GENIE3/inst/doc/GENIE3.html

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@Leite

Thanks for replying I will try set threshold as you said

Kind regards

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