CSB_RNs

Procedure flow for drug target discovery

一、example codes

1、Download the chip data in the GEO database and annotate it

profilerFrame <- get.GEO.data(GEO.acession = "28735",platfrom = "GPL6244")
#profilerFrame is the data.frame data type, behavioral gene, and gene expression profile data listed in the sample.
#There are not many chip platforms that can be annotated automatically, so you can experiment and do it yourself.tabel.1
profilerFrame

2、Plot the boxplot plot to observe the data outline

boxplot(profilerFrame,col="gray",xlab="samples",ylab="express label",main="expression quentity boxplt")

3、Filter the data according to the entropy value, remove the blank rows, all 0 rows

profilerFramecleaned<-geneentropyfilter(profilerFrame)

4、The expression profile data were analyzed according to the classification

profileData <- analysisIt(profilerFrame,sample.label = c(rep(c(1,0),times=45)))

5、Draw a volcano map according to the threshold

volcanoPlot(profileData)

5、Plot the barplot of enrichment analysis

geneSet <- rownames(profileData@data)[profileData@selected.gene]
plotGOtermsbarplot(geneSet = geneSet)

6、Calculate the parameters of the protein network exported from the string database

net <- read.table("./string_interactions.tsv",header = T)
netParameters <-getNetParameters(net)
CSB_RNs(profileData,netParameters)

二、installation

install.packages("devtools")
library(devtools)
install_github("liuxingyi/CSB_RNs")

#load installed packages
library("targetFinder")

appendix

table.1 Chip platform that can be annotated

gpl	Organism	bioc_package
GPL32	"Mus musculus"	mgu74a
GPL33	"Mus musculus"	mgu74b
GPL34	"Mus musculus"	mgu74c
GPL74	"Homo sapiens"	hcg110
GPL75	"Mus musculus"	mu11ksuba
GPL76	"Mus musculus"	mu11ksubb
GPL77	"Mus musculus"	mu19ksuba
GPL78	"Mus musculus"	mu19ksubb
GPL79	"Mus musculus"	mu19ksubc
GPL80	"Homo sapiens"	hu6800
GPL81	"Mus musculus"	mgu74av2
GPL82	"Mus musculus"	mgu74bv2
GPL83	"Mus musculus"	mgu74cv2
GPL85	"Rattus norvegicus"	rgu34a
GPL86	"Rattus norvegicus"	rgu34b
GPL87	"Rattus norvegicus"	rgu34c
GPL88	"Rattus norvegicus"	rnu34
GPL89	"Rattus norvegicus"	rtu34
GPL91	"Homo sapiens"	hgu95av2
GPL92	"Homo sapiens"	hgu95b
GPL93	"Homo sapiens"	hgu95c
GPL94	"Homo sapiens"	hgu95d
GPL95	"Homo sapiens"	hgu95e
GPL96	"Homo sapiens"	hgu133a
GPL97	"Homo sapiens"	hgu133b
GPL98	"Homo sapiens"	hu35ksuba
GPL99	"Homo sapiens"	hu35ksubb
GPL100	"Homo sapiens"	hu35ksubc
GPL101	"Homo sapiens"	hu35ksubd
GPL201	"Homo sapiens"	hgfocus
GPL339	"Mus musculus"	moe430a
GPL340	"Mus musculus"	mouse4302
GPL341	"Rattus norvegicus"	rae230a
GPL342	"Rattus norvegicus"	rae230b
GPL570	"Homo sapiens"	hgu133plus2
GPL571	"Homo sapiens"	hgu133a2
GPL886	"Homo sapiens"	hgug4111a
GPL887	"Homo sapiens"	hgug4110b
GPL1261	"Mus musculus"	mouse430a2
GPL1352	"Homo sapiens"	u133x3p
GPL1355	"Rattus norvegicus"	rat2302
GPL1708	"Homo sapiens"	hgug4112a
GPL2891	"Homo sapiens"	h20kcod
GPL2898	"Rattus norvegicus"	adme16cod
GPL3921	"Homo sapiens"	hthgu133a
GPL4191	"Homo sapiens"	h10kcod
GPL5689	"Homo sapiens"	hgug4100a
GPL6097	"Homo sapiens"	illuminaHumanv1
GPL6102	"Homo sapiens"	illuminaHumanv2
GPL6244	"Homo sapiens"	hugene10sttranscriptcluster
GPL6947	"Homo sapiens"	illuminaHumanv3
GPL8300	"Homo sapiens"	hgu95av2
GPL8490	"Homo sapiens"	IlluminaHumanMethylation27k
GPL10558	"Homo sapiens"	illuminaHumanv4
GPL11532	"Homo sapiens"	hugene11sttranscriptcluster
GPL13497	"Homo sapiens"	HsAgilentDesign026652
GPL13534	"Homo sapiens"	IlluminaHumanMethylation450k
GPL13667	"Homo sapiens"	hgu219
GPL15380	"Homo sapiens"	GGHumanMethCancerPanelv1
GPL15396	"Homo sapiens"	hthgu133b
GPL17897	"Homo sapiens"	hthgu133a

The tool is developed by Xingyi Liu, for questions and comments please contact email--liuxingyisw@outlook.com