Question: miRNA_ID to GENE_SYMBOL conversion
0
gravatar for minoo
3.4 years ago by
minoo0
minoo0 wrote:

I have a list of miRNA IDs and a list of mRNA IDs. I have converted the list of mRNA IDs to gene symbols by a list of data that was exist in NCBI and miRNA IDs list to gene symbols by http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index but I got in trouble because gene symbols on NCBI didn't match to gene symbols exist in Diana site . Can anyone tell me a good way to transform both mRNA & miRNA lists to a platform like unigene that would be unique in all kinds of databases?

rna-seq gene genome • 1.8k views
ADD COMMENTlink modified 2.6 years ago by Denise - Open Targets5.0k • written 3.4 years ago by minoo0
0
gravatar for Rajesh Detroja
3.4 years ago by
INDIA
Rajesh Detroja60 wrote:

Dear minoo,

If you have to convert GENE SYMBOL of miRNA for HUMAN then you can download one file name like "mirDIP-All-Data-Version1.0.txt" from http://ophid.utoronto.ca/mirDIP/download.jsp. This file contains GENE SYBMOL of human miRNAs like as example given Below :

MICRORNA    GENE_SYMBOL SOURCE  RANK    
hsa-mir-708 NNAT    PITA Top Targets    top_1_percent   
hsa-mir-1207-5p C2orf17 PITA Top Targets    top_1_percent   
hsa-mir-574-5p  KLF7    PITA Top Targets    top_1_percent   
hsa-mir-574-5p  FLJ46831    PITA Top Targets    top_1_percent   
hsa-mir-939 GRIN2D  PITA Top Targets    top_1_percent   
hsa-mir-1207-5p C1orf34 PITA Top Targets    top_1_percent   
hsa-mir-939 LOC56901    PITA Top Targets    top_1_percent   
hsa-mir-1268    C1orf55 PITA Top Targets    top_1_percent   
hsa-mir-939 THRA    PITA Top Targets    top_1_percent   
hsa-mir-663 NFIX    PITA Top Targets    top_1_percent
ADD COMMENTlink written 3.4 years ago by Rajesh Detroja60

Thanks , but organism of my data is Mus musculus.

ADD REPLYlink written 3.4 years ago by minoo0
0
gravatar for Denise - Open Targets
2.6 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

Ensembl BioMart could help you. There may not be unigene IDs for the miRNAs but you can get the MGI IDs which is the official gene name (and symbol) for mouse genes. This is a query that can help you:

<query virtualschemaname="default" formatter="TSV" header="0" uniquerows="0" count="" datasetconfigversion="0.6" &gt;<="" p="">

<Dataset name = "mc57bl6nj_gene_ensembl" interface = "default" >
    <Filter name = "chromosome_name" value = "1"/>
    <Filter name = "biotype" value = "miRNA"/>
    <Attribute name = "ensembl_gene_id" />
    <Attribute name = "ensembl_transcript_id" />
    <Attribute name = "unigene" />
    <Attribute name = "mgi_symbol" />
</Dataset>

</query>

ADD COMMENTlink written 2.6 years ago by Denise - Open Targets5.0k
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