Convert miRNA_ID to GENE-symbol

Question

[sorour.hasani]

Hi everybody

I want to calculate DEGs for my data microarray and then run them in the enrichment pathway. I do not know how to convert miRNA_ID to gene_symbol. I examined miRBase and Norwalk, but they illustrate some gene symbol for one miRna. I can't handle the problem. Is there any command or coding to run in R? miRNA ID example: hsa-miR-223

[GenoMax]

Provide examples of ID's when asking questions about them.

[i.sudbery]

Hi. Its not entirely clear what you are looking for miR-233 is the gene symbol for this microRNA (sometimes written MIR223).

[sorour.hasani]

hi

I have a list of miRNA ID from GEO2R, I have to convert them to gene symbol to calculate WGCN and DEG calculation. I convert them to ENSMBLE but when I want to use biomart to convert them to gene symbol i faced errors that i cannot handel it.

my list:

ENSG00000199121
ENSG00000284353
ENSG00000207696
ENSG00000207993
ENSG00000284353
ENSG00000284567
ENSG00000207781
ENSG00000207637
ENSG00000283798
ENSG00000199122 
ENSG00000221641
ENSG00000221410
ENSG00000283871
ENSG00000267195

x<-read.delim(file="data/s.txt",header=T)
x.df <- as.data.frame(x)
x.df


x.df$SYMBOL <- mapIds(org.Hs.eg.db,   
                      keys = rownames(x.df),   
                      keytype = "ENSEMBL",   
                      column = "SYMBOL") 

when i run this i get this error:

Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.

---

when I use this code:

mart <- useMart("ensembl","hsapiens_gene_ensembl")

genes <- getBM(attributes=c("ensembl_transcript_id","external_gene_name","ensembl_gene_id","hgnc_symbol",),
                           filters = "ensembl_transcript_id",
                           values = data, 
                           mart = mart)

rownames(genes) <- genes$ensembl_transcript_id
names(genes) = c("transcript_id", "gene_name", "gene_id",)

I get hugo symbol, I want gene_symbol..................

[Arup Ghosh]

Share a snippet of the data [ use head(x.df) ].

gList <- c("ENSG00000199121", "ENSG00000284353", "ENSG00000207696", "ENSG00000207993", "ENSG00000284353", "ENSG00000284567")
AnnotationDbi::select(org.Hs.eg.db, 
                      keys = gList,  
                      columns = c("GENENAME", "ENTREZID", "ALIAS", "UNIPROT"),
                      keytype = "ENSEMBL")

This should return the miRNA names and aliases like the following.

           ENSEMBL     GENENAME ENTREZID       ALIAS UNIPROT
1  ENSG00000199121 microRNA 26b   407017     MIRN26B    <NA>
2  ENSG00000199121 microRNA 26b   407017 hsa-mir-26b    <NA>
3  ENSG00000199121 microRNA 26b   407017     miR-26b    <NA>
4  ENSG00000199121 microRNA 26b   407017      MIR26B    <NA>
5  ENSG00000284353 microRNA 142   406934     MIRN142    <NA>
6  ENSG00000284353 microRNA 142   406934     mir-142    <NA>
7  ENSG00000284353 microRNA 142   406934      MIR142    <NA>
8  ENSG00000207696 microRNA 659   724029     MIRN659    <NA>
9  ENSG00000207696 microRNA 659   724029 hsa-mir-659    <NA>
10 ENSG00000207696 microRNA 659   724029     mir-659    <NA>

[GenoMax]

I get hugo symbol, I want gene_symbol.

HGNC is the organization under HUGO that approves symbols for human genes.

Are you perhaps looking for alias names like what @Arup has shown?

[i.sudbery]

Hmmm.... Those alias's look like a mixture of HGNC gene symbols, miRBase miRNAnames, and.... I don't know what the third ones are... Perhaps rnacentral names? I'm also no sure on the difference between things like MIRN26B and MIR26B - some of these Ensembl IDs seem to be associated with both.

Take ENSG00000199121 above. MIR26B is the HGNC symbol, hsa-mir-26b is the miRBase name, miR-26B and MIRN26b i don't know the original of. You could also add to that the miRBase ID, which is MI0000084, the entrez gene id, which is 407017 and the ReqSeq transcript id, which is NR_029500.1.

I'm not clear which of these you are starting with and which you want to convert to (i'm also not clear why you need it for DEGs, and I've never heard of doing WGCN with miRNAs).