No result in enrichGO

Question

[sugus]

Hi, I am new to clusterProfiler and following the R documentation.

In the website instruction for enrichplot, here is some demo for enrichGO:

library(clusterProfiler)
data(geneList, package="DOSE")
de <- names(geneList)[abs(geneList) > 2]
ego <- enrichGO(de, OrgDb = "org.Hs.eg.db", ont="BP", readable=TRUE)
library(enrichplot)
goplot(ego)

And I just use this but get no results. Here is my code:

library(clusterProfiler)
library(org.Hs.eg.db)
library(DOSE)
data(geneList)
de <- names(geneList)[abs(geneList) > 2]
ego <- enrichGO(de, OrgDb = "org.Hs.eg.db", ont="BP", readable=TRUE)
head(summary(ego))

and I get:

> head(summary(ego))
[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust    qvalue      geneID      Count      
<0 rows> (or 0-length row.names)
Warning message:
In summary(ego) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.

So, what's wrong about my performance? Could anyone give me a hint.

Answer 1

[szhaoaf]

Hey!

Could you please show me with your contents of 'de', the input of your enrichGo command.

Because for my case, I will try to change my gene ID from 'ensembl_ID' to 'entrezid' to get more mapping results.

Since you got nothing mapping results, I guess there is something wrong in your input genes.

Group_4 enriched Go terms

group4_top100_gene<- as.character((markergenes$Ensembl_ID)[9920:10019])

ID <- bitr(group4_top100_gene, fromType="ENSEMBL", toType="ENTREZID", OrgDb="org.Dr.eg.db")

head(ID)

ego <- enrichGO(gene = as.vector(ID$ENTREZID), OrgDb=org.Dr.eg.db, ont = "BP", minGSSize = 1, pvalueCutoff = 0.05, qvalueCutoff = 1, readable = TRUE) head(summary(ego))

dim(ego)

result <- simplify(ego, cutoff=0.7, by="p.adjust", select_fun=min)

barplot(result, showCategory=10,title="GO terms enriched in group_4")

dotplot(result,showCategory=15,title="GO terms enriched in group_4") dim(result)

Bests Shizheng

[sugus]

Sure, here is the contents:

> de
  [1] "4312"   "8318"   "10874"  "55143"  "55388"  "991"    "6280"   "2305"   "9493"   "1062"   "3868"  
 [12] "4605"   "9833"   "9133"   "6279"   "10403"  "8685"   "597"    "7153"   "23397"  "6278"   "79733" 
 [23] "259266" "1381"   "3627"   "27074"  "6241"   "55165"  "9787"   "7368"   "11065"  "55355"  "9582"  
 [34] "220134" "55872"  "51203"  "3669"   "83461"  "22974"  "10460"  "10563"  "4751"   "6373"   "8140"  
 [45] "79019"  "820"    "10635"  "1844"   "4283"   "27299"  "55839"  "27338"  "890"    "9415"   "983"   
 [56] "54821"  "10232"  "4085"   "6362"   "9837"   "5080"   "7850"   "81930"  "5918"   "81620"  "332"   
 [67] "55765"  "79605"  "3832"   "6286"   "5163"   "2146"   "3002"   "50852"  "7272"   "2568"   "64151" 
 [78] "51806"  "366"    "2842"   "9212"   "140578" "51659"  "8715"   "4902"   "8208"   "1111"   "9319"  
 [89] "9055"   "3833"   "146909" "23475"  "4321"   "11182"  "10112"  "3902"   "3620"   "3887"   "51514" 
[100] "6790"   "4521"   "891"    "57110"  "8544"   "1448"   "24137"  "6355"   "10578"  "4174"   "9232"  
[111] "643314" "1307"   "776"    "4129"   "9370"   "196740" "25924"  "8857"   "1602"   "51161"  "3708"  
[122] "23090"  "10742"  "51760"  "9122"   "10699"  "8416"   "60598"  "79148"  "64799"  "4629"   "1556"  
[133] "55096"  "26289"  "6038"   "771"    "51313"  "23704"  "3117"   "80129"  "23158"  "125"    "4958"  
[144] "4857"   "1311"   "5105"   "5174"   "730"    "2018"   "81563"  "2532"   "1308"   "4250"   "23362" 
[155] "2167"   "51705"  "2593"   "652"    "80736"  "4036"   "57502"  "5507"   "56521"  "22885"  "4137"  
[166] "8483"   "8839"   "2066"   "4693"   "4148"   "79083"  "1101"   "3158"   "3169"   "5346"   "1408"  
[177] "9547"   "2922"   "11283"  "64499"  "54829"  "1524"   "10234"  "1580"   "10647"  "25893"  "24141" 
[188] "10351"  "2330"   "5304"   "79846"  "8614"   "2625"   "7021"   "7802"   "79689"  "11122"  "55351" 
[199] "9"      "4239"   "5241"   "10551"  "10974"  "79838"  "79901"  "57758"  "4969"

There code is from the website instruction and I think the default process uses entrez_id.

[szhaoaf]

Hey Sugus,

I just tried your codes and it works well.

library(clusterProfiler)
library(org.Hs.eg.db)
de<-c("4312","8318","10874","55143","55388","991")
ego <- enrichGO(de, OrgDb = "org.Hs.eg.db", ont="BP", readable=TRUE)
head(summary(ego))

ID                          Description GeneRatio   BgRatio       pvalue   p.adjust      qvalue      geneID Count

GO:0006270 GO:0006270 DNA replication initiation 2/6 42/17381 8.498316e-05 0.01453212 0.006440829 CDC45/MCM10 2 GO:0007062 GO:0007062 sister chromatid cohesion 2/6 133/17381 8.543746e-04 0.04335978 0.019217629 CDCA8/CDC20 2 GO:0000070 GO:0000070 mitotic sister chromatid segregation 2/6 142/17381 9.730351e-04 0.04335978 0.019217629 CDCA8/CDC20 2 GO:0006261 GO:0006261 DNA-dependent DNA replication 2/6 145/17381 1.014264e-03 0.04335978 0.019217629 CDC45/MCM10 2 GO:0000819 GO:0000819 sister chromatid segregation 2/6 230/17381 2.525189e-03 0.04962063 0.021992521 CDCA8/CDC20 2 GO:0140014 GO:0140014 mitotic nuclear division 2/6 253/17381 3.045861e-03 0.04962063 0.021992521 CDCA8/CDC20 2

Warning message:

In summary(ego) : summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.

[sugus]

Yes, it works today. So weird.....

[WF]

Dear all,

I'm trying to run groupGO, but its return "no count, noGeneRatio and no geneID but just a list as shown below:

"ID" "Description" "Count" "GeneRatio" "geneID" "GO:0005886" "GO:0005886" "plasma membrane" 0 "0/0" "" "GO:0005628" "GO:0005628" "prospore membrane" 0 "0/0" "" "GO:0005789" "GO:0005789" "endoplasmic reticulum membrane" 0 "0/0" "" "GO:0019867" "GO:0019867" "outer membrane" 0 "0/0" "" "GO:0031090" "GO:0031090" "organelle membrane" 0 "0/0" "" "GO:0034357" "GO:0034357" "photosynthetic membrane" 0 "0/0" "" "GO:0036362" "GO:0036362" "ascus membrane" 0 "0/0" ""

and return "No gene can be mapped" when I ran enrichGO after this.

Can anyone please assist? let say I have a gene list "Erf","Cdh22","Arhgap8","Rab11fip4","Mn1","Grb10","Ehbp1" for rat?

Appreciate that.

Best wishes, WF

Answer 2

[munizmom]

Hi, Just type the following head(summary(as.data.frame(ego))).It should work

[sugus]

No, this code just makes a more decent summary, but the result is still nothing.