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Question: I want to order genes in GO groups
0
gravatar for kanacska
2.2 years ago by
kanacska10
Hungary
kanacska10 wrote:

Hi!

I have a list of genes, but i a havent got any values for the genes. I want to put the genes in GO(gene onthology) groups. How can i do that without any values??

 

Thanks,

Anna

ADD COMMENTlink modified 2.2 years ago by b.nota290 • written 2.2 years ago by kanacska10
1
gravatar for b.nota
2.2 years ago by
b.nota290
Netherlands
b.nota290 wrote:

You are not easily satisfied, are you? ;P

There are probably more sophisticated ways, but here's one way to get what you asked for.

list<-c("Slc25a1","Casr")
GOs <- stack(getgo(list,'mm9','geneSymbol'))
GOs.terms<-Term(GOs$values)
GOs.terms<-as.matrix(GOs.terms)
GOs.with.terms<-cbind(GOs,GOs.terms)
GOs.with.terms<-as.matrix(GOs.with.terms)
GOs.with.terms.calcium<-GOs.with.terms[grep("calcium",GOs.with.terms[,3]),]

 

 

ADD COMMENTlink written 2.2 years ago by b.nota290
1

Yeah ive deserved that...sorry:S

Thank you very very much!!

Anna

ADD REPLYlink written 2.1 years ago by kanacska10
0
gravatar for b.nota
2.2 years ago by
b.nota290
Netherlands
b.nota290 wrote:
library(goseq)
list<- c("BRCA1","BRCA2")
GOs <- stack(getgo(list,'hg19','geneSymbol'))
ADD COMMENTlink written 2.2 years ago by b.nota290
0
gravatar for kanacska
2.2 years ago by
kanacska10
Hungary
kanacska10 wrote:

Thank you!

 

Oh ive forgotten to wright down that i want to do it with mouse genes and iv tried:

list<- c("y","x")
GOs <- stack(getgo(list,'mm9','geneSymbol'))

 

But it doesnt work... Is there a way to put mouse genes in GO categories??

 

Thank u!

 

Anna

ADD COMMENTlink written 2.2 years ago by kanacska10

Are 'x' and 'y' mouse gene symbols?
 

ADD REPLYlink written 2.2 years ago by James W. MacDonald45k
0
gravatar for kanacska
2.2 years ago by
kanacska10
Hungary
kanacska10 wrote:

x and y equals a gene symbol like x = Lbx1 , y= Hoxd9

 

ADD COMMENTlink written 2.2 years ago by kanacska10
0
gravatar for b.nota
2.2 years ago by
b.nota290
Netherlands
b.nota290 wrote:

Is this library installed?

org.Mm.eg.db

Maybe you should post your error and script lines if you want some help here.

ADD COMMENTlink written 2.2 years ago by b.nota290
0
gravatar for kanacska
2.2 years ago by
kanacska10
Hungary
kanacska10 wrote:

Hi.

 

Now its working: 

GOs <- stack(getgo(list,'mm9','geneSymbol'))

And now i get a realy long list of genes with GO annotation. Is there any easy way to filter for GO-s which are associated with calcium signalization, calcium transport etc. Here is a part of the list of the results:

 

................

"166"    "GO:0044212"    "Alx1"
"167"    "GO:0046982"    "Alx1"
"168"    "GO:0046983"    "Alx1"
"169"    "GO:0097159"    "Alx1"
"170"    "GO:1901363"    "Alx1"
"171"    "GO:0001501"    "Alx3"
"172"    "GO:0006139"    "Alx3"
"173"    "GO:0006351"    "Alx3"
"174"    "GO:0006355"    "Alx3"
"175"    "GO:0006725"    "Alx3"
"176"    "GO:0006807"    "Alx3"

...................

ADD COMMENTlink written 2.2 years ago by kanacska10
0
gravatar for b.nota
2.2 years ago by
b.nota290
Netherlands
b.nota290 wrote:
list<-c("Slc25a1","Casr")
GOs <- stack(getgo(list,'mm9','geneSymbol'))
GOs.terms<-Term(GOs$values)
GOs.terms.calcium<-grep('calcium',GOs.terms,value=TRUE)

 

ADD COMMENTlink written 2.2 years ago by b.nota290
0
gravatar for kanacska
2.2 years ago by
kanacska10
Hungary
kanacska10 wrote:

Thank you!

 

There is a thing which, I dont understand i had two gene list one with mouse homeobox genes and the other one which is a gene list of mouse mesenchymal stem cell markers. The frist one worked with:

 library(goseq)

list<- c("Alx1", "Alx3", "Alx4")
GOs <- stack(getgo(list,'mm9','geneSymbol'))

the second one didnt(mouse MSC markers)

 library(goseq)

list2<- c("Abcb1a", "Alcam", "Anpep")

GOsa <- stack(getgo(list2,'mm9','geneSymbol'))

The error message is: Warning message:
In stack.default(getgo(list2, "mm9", "geneSymbol")) :
  non-vector elements will be ignored

I dont understand what does the message mean, the genes are mouse genes and i dont known why it doesnt work...

Thank you,

Anna

ADD COMMENTlink written 2.2 years ago by kanacska10
0
gravatar for b.nota
2.2 years ago by
b.nota290
Netherlands
b.nota290 wrote:

Hi Anna,

When I copy-paste your lines in R:

list2<- c("Abcb1a", "Alcam", "Anpep")

GOsa <- stack(getgo(list2,'mm9','geneSymbol'))

I do not get the error.

dim(GOsa)
[1] 381   2

Is it a warning or error message? Can you check whether you have created your GOsa object?

ADD COMMENTlink written 2.2 years ago by b.nota290
0
gravatar for kanacska
2.2 years ago by
kanacska10
Hungary
kanacska10 wrote:

Ah it eventually worked, thank you:) Its my last question ive never filtered from a list.. now that i have the Goterms which is associated with calcium, i want to which gene sare in the calcium associated GOs. Ive tried to merge the list with the GOs.terms but nothing (my lists contains more genes than three, thats just an example) How can I filter out that which genes are in calcium associated GOs??

ADD COMMENTlink written 2.2 years ago by kanacska10
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