Hi,
I have PDX expression data,and I calculated the fpkms of human and mouse reads separately. I want to look at the expression levels of mouse genes in the human reads.
So I have to convert the mouse gene names to human gene names.
I looked at this post, but there is not much information present here.
Best,
Ron
4 answers
Mouse/human gene homologs: http://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt
You can try following function:
musGenes <- c("Hmmr", "Tlx3", "Cpeb4")
### Basic function to convert mouse to human gene names
convertMouseGeneList <- function(x){
require("biomaRt")
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
genesV2 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = x , mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T)
humanx <- unique(genesV2[, 2])
### Print the first 6 genes found to the screen
print(head(humanx))
return(humanx)
}
convertMouseGeneList(musGenes)
In case someone comes across this (as I just did): this can be done using Ensembl biomart.
E.g. select Mouse genes database, and under attributes > homologous you select your species of interest.
The homologs given by genomax are rather strict - for instance, GZMB doesn't map to Gzmb. Here's instructions for how to get orthologous genes from biomart (obtain a flat file via web interface). http://www.ensembl.info/blog/2009/01/21/how-to-get-all-the-orthologous-genes-between-two-species/
If anyone has example code to do this using biomaRt I would be very interested.
Per HGNC guidelines proper way to represent human gene names is by using upper case letters and numbers. These also apply to some other vertebrate genomes.
Since the table (the link above has been updated, Aug 2017).
I thought the HGNC guidelines only apply to human. As far as I know, the mouse nomenclature has the first letter capitalized followed by lower case letters. Have there been recent changes to the official nomenclatures for model organisms ?
You are correct in case of mouse. These are the guidelines for mouse gene names.
VGNC is managing names for chimpanzee, horse, cow and dog based on orthology to humans.
You may already have seen this: https://www.r-bloggers.com/converting-mouse-to-human-gene-names-with-biomart-package/
nichenetr package can easily convert mouse to human:
library(nichenetr)
mmGenes <- c('Ms4a1', 'Cd8a')
hsaGenes <- convert_human_to_mouse_symbols(mmGenes)
or human to mouse
hsaGenes <- c('MS4A1', 'CD8A')
mmGenes <- convert_mouse_to_human_symbols(hsaGenes)
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What type of id's do you have? Ensembl, UCSC, Unigene, RefSeq, HUGO?
I have gene symbols.Can I just convert them to Upper Case?for e.g Psarp gene in mouse is present as PSARP in humans.
I found lot of genes as such.
In general yes, names are equal just putting in uppercase all letters. For missing genes you can check them individually in UCSC Genome Browser or Ensembl if they are a few.
Don't do this. Although most orthologous genes between human and mouse share the same gene symbol, this may not always be true especially if the symbols come from different genome annotations (e.g. different versions of Ensembl or Ensembl vs NCBI). A mouse gene and a human gene may share the same symbol and not be orthologous for various reasons. The proper way is to map genes by orthology. There have already been several posts on the subject, including the one you've linked to.
ok, I agree, names could be the same but the genes could be non-orthologs. A list of precomputed pairs will be better.