I want to order genes in GO groups
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kanacska ▴ 10
@kanacska-7375
Last seen 5.6 years ago
Hungary

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

gene ontology genefilter • 1.2k views
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b.nota ▴ 340
@bnota-7379
Last seen 7 months ago
Netherlands

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]),]

 

 

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Yeah ive deserved that...sorry:S

Thank you very very much!!

Anna

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b.nota ▴ 340
@bnota-7379
Last seen 7 months ago
Netherlands
library(goseq)
list<- c("BRCA1","BRCA2")
GOs <- stack(getgo(list,'hg19','geneSymbol'))
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kanacska ▴ 10
@kanacska-7375
Last seen 5.6 years ago
Hungary

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

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Are 'x' and 'y' mouse gene symbols?
 

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kanacska ▴ 10
@kanacska-7375
Last seen 5.6 years ago
Hungary

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

 

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b.nota ▴ 340
@bnota-7379
Last seen 7 months ago
Netherlands

Is this library installed?

org.Mm.eg.db

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

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kanacska ▴ 10
@kanacska-7375
Last seen 5.6 years ago
Hungary

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"

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

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b.nota ▴ 340
@bnota-7379
Last seen 7 months ago
Netherlands
list<-c("Slc25a1","Casr")
GOs <- stack(getgo(list,'mm9','geneSymbol'))
GOs.terms<-Term(GOs$values)
GOs.terms.calcium<-grep('calcium',GOs.terms,value=TRUE)

 

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kanacska ▴ 10
@kanacska-7375
Last seen 5.6 years ago
Hungary

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

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b.nota ▴ 340
@bnota-7379
Last seen 7 months ago
Netherlands

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?

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kanacska ▴ 10
@kanacska-7375
Last seen 5.6 years ago
Hungary

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??

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