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?
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
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" ><="" 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>