netGO-Data

This repository contains pre-calculated R object files for demo use.

netGO ( Calculation )

To run netGO, four input data are required as follows: genes, genesets, network, genesetV.

Usage table

Human (in human directory)

Data	genes	genesets	network	genesetV
Breast Tumor	brca.RData	c2gs.RData	networkString.RData networkHumannet.RData	genesetVString1,2.RData genesetVHumannet1,2.RData
P53	p53.RData	c2gs.RData	networkString.RData networkHumannet.RData	genesetVString1,2.RData genesetVHumannet1,2.RData
Diabetes	dg.RData	cpGenesets.RData	networkString.RData networkHumannet.RData	cpgenesetV1,2.RData

for c5 gene-sets ( gene ontology ), use c5gs.RData and c5genesetV 1~7.RData ( it's string based )

dgans.Rdata is standard positive gene-sets for Diabetes
brcaans.Rdata is standard positive gene-sets for Breast Tumor

or the user can use Breast Tumor data using DownloadExampleData function in netGO (Recommended)

Arabidopsis thaliana

Data	genes	genesets	network	genesetV
ShadowResponse	Aragenes.RData	KEGGara.RData	networkAranet.RData	AragenesetV.RData

Important

The original genesetV.RData (>25Mb) file was splitted into two to upload to github
So they should be combined using rbind. For example,

load("genesetVString1.RData") # load genesetV1
load("genesetVString2.RData") # load genesetV2
genesetV = rbind(genesetV1,genesetV2)
rm(genesetV1,genesetV2) # for clear memory usage, optional

netGOVis (Visualization)

netGOVis function requires four data as follows : obj, genes, genesets, network

Usage table

Data	obj	genes	genesets	network
BreastTumor	brcaresult.RData	brca.RData	c2gs.RData	networkString.RData
ShadowResponse	shadowResult.RData	Aragenes.RData	KEGGara.RData	networkAranet.RData

Note that pre-calculated brcaresult is built for brca[1:30], so only brca[1:30] should be used.

Sources of data (version omitted)

Genes

Human : BreastTumor, P53, Diabete
Yeast : ShadowResponse

Gene-sets

mSigDB, KEGG

Networks

stringDB, HumanNet, AraNet, YeastNet, MouseNet

Question / Comment / Suggestion : kjh0530@unist.ac.kr, dougnam@unist.ac.kr

Thanks.