Question: GSEA analysis with Mouse (Please give some comments..)
0
gravatar for illinois.ks
4.7 years ago by
illinois.ks160
Korea, Republic Of
illinois.ks160 wrote:

Hello all,

I am doing GSEA analysis. I have done with human sucessfully. 

However, this time, I am trying to run with my mouse gene. .I realized that thse mSIG DB are annotated with only human.. I donwloaded the msigDB for mouse from genepattern website.

Howver, GSEA program didn't allow me to use this downloaded data for my analysis... 

Could you please someone help me with this?  T.T 

I am creating with my ***.rnk (rank file) for this analysis.. 

 

gsea; mouse; • 9.3k views
ADD COMMENTlink modified 14 days ago by ATpoint30k • written 4.7 years ago by illinois.ks160
1

I will try to capitalize all my mouse genes. Sometimes, it can fool the software to treat the mouse gene as human gene. If you want a even better approach, you can check the homology and convert the mouse to human. Usually capitalize are simple enough.

ADD REPLYlink written 4.7 years ago by Sam2.6k

Thnk you so much!

yEs. I will try.. :) 

ADD REPLYlink written 4.7 years ago by illinois.ks160
1
gravatar for igor
4.7 years ago by
igor9.6k
United States
igor9.6k wrote:

Jackson Lab has the Vertebrate Homology resource for converting between homologous human and mouse genes (most of the time, it's just adjusting the case).

Update: you can also try msigdbr which already solved the multi-species conversion issue (there are a number of caveats to the process that are not very obvious): MSigDB for Multiple Organisms in a Tidy Data Format

ADD COMMENTlink modified 14 days ago • written 4.7 years ago by igor9.6k
1
gravatar for AidanQuinn
2.3 years ago by
AidanQuinn40
United States
AidanQuinn40 wrote:

Generally I use Ensembl Biomart (but you can substitute your favorite gene ID conversion tool here) to convert all of the gene names in each gene signature in the *.gmx or *.gmt, from human to mouse. I then use the mouse IDs to make a custom *.gmx or *.gmt file.

It's convenient to do this in R if you know how but not necessary, it works perfectly well do to copy-paste into the web interface.

Word of warning: look out for genes that don't convert using automated tools. Often you will come across genes that actually do have mouse orthologs but are not annotated in Biomart. You can manually add these genes to the signatures by a quick Google search.

ADD COMMENTlink modified 17 days ago by ATpoint30k • written 2.3 years ago by AidanQuinn40
1
gravatar for sissypants :)
14 days ago by
sissypants :)10 wrote:

Have a look at the msigdbr R package. It easily converts mouse gene names to human homolog equivalents.

ADD COMMENTlink written 14 days ago by sissypants :)10
1
gravatar for ATpoint
14 days ago by
ATpoint30k
Germany
ATpoint30k wrote:

Here is a solution using biomaRt (in R) from Ensembl which creates a table that lists all mouse genes and the respective human orthologs. Credits mainly to Dave Tang's blog where the idea is from.

library(biomaRt)

Mouse2Human <- function(MouseGenes){

  human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")

  genesMousetoHuman = getLDS(attributes = c("ensembl_gene_id","mgi_symbol"), 
                             filters = "mgi_symbol", 
                             values = MouseGenes , 
                             mart = mouse, 
                             attributesL = c("ensembl_gene_id", "hgnc_symbol"), 
                             martL = human, 
                             uniqueRows = TRUE)

  colnames(genesMousetoHuman) <- c("Mouse.Gene_ID", "MGI", "Human.Gene_ID", "HGNC")

  return(genesMousetoHuman) 

}

## Get mouse genes
mmusculus_genes <- getBM(attributes = c("ensembl_gene_id", "mgi_symbol"),  
                         mart = useMart("ensembl", dataset = "mmusculus_gene_ensembl"),
                         useCache = FALSE)

## create the conversion table
Mouse2HumanTable <- Mouse2Human(MouseGenes = mmusculus_genes$mgi_symbol)

Output:

> Mouse2HumanTable
         Mouse.Gene_ID           MGI   Human.Gene_ID           HGNC
1   ENSMUSG00000070979        Actl7a ENSG00000187003         ACTL7A
2   ENSMUSG00000069911       Insyn2b ENSG00000204767        INSYN2B
3   ENSMUSG00000028173           Wls ENSG00000116729            WLS
4   ENSMUSG00000094356      Igkv8-28 ENSG00000211598        IGKV4-1
5   ENSMUSG00000104769      Igkv8-34 ENSG00000211598        IGKV4-1
6   ENSMUSG00000076581      Igkv8-26 ENSG00000211598        IGKV4-1
7   ENSMUSG00000095794      Igkv6-17 ENSG00000211598        IGKV4-1
8   ENSMUSG00000064370       mt-Cytb ENSG00000198727         MT-CYB
9   ENSMUSG00000022099          Dmtn ENSG00000158856           DMTN
10  ENSMUSG00000033717        Adra2a ENSG00000150594         ADRA2A
11  ENSMUSG00000022016        Akap11 ENSG00000023516         AKAP11
(...)
ADD COMMENTlink modified 14 days ago • written 14 days ago by ATpoint30k

You don't need this line within the Mouse2Human function:

MouseGenes <- as.character(mmusculus_genes$mgi_symbol)

If it is to deal with a scenario where MouseGenes is undefined, mmusculus_genes will need to be initialized within the function as well, or the function ends up having undeclared dependencies.

ADD REPLYlink written 14 days ago by RamRS25k

You're right, not sure how this non-sense line made it in there. Edited.

ADD REPLYlink written 14 days ago by ATpoint30k
0
gravatar for atakanekiz
14 days ago by
atakanekiz190
atakanekiz190 wrote:

I tried GSEA with mouse data both by mapping the homologs using a proper method (ensembl/biomaRt as suggested here), and also by simply converting sentence case gene names (i.e. Pdcd1) to upper case (i.e. PDCD1). In my experience, these approaches work similarly.

Using uppercase letters, for the most part, works because human gene names are simply a capitalized version of mouse genes. Although this "conversion" may result in losing a few genes, since you are looking at a constellation of genes in GSEA, I don't think it is a big problem.

ADD COMMENTlink written 14 days ago by atakanekiz190
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