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How To Convert Refseq Id To Gene Symbol For Non-Coding Rnas

Hi,

i'm trying to generate a full gene annotation table with corresponding gene symbols/gene descriptions and other gene IDs(ucscknown gene id, entrezid, ensembl id) to refseqID for ncRNAs as well as protein coding genes. it seems kgXref table generates such annotations for only prefix NM* protein coding genes. not NR*.

I would like to get as

e.g ucsc known id, entrezid, ensembl id, NR_045294(RefseqID), Gm4285(gene symbol), Mus musculus predicted gene 4285, non-coding RNA(gene description)

any thoughts?

non rna annotation database
• 8,479 views • link
updated by Curiosity • Curiosity • written by Hamilton • Hamilton

2 answers

You could use the following XSLT stylesheet:

<xsl:stylesheet version="1.0" xmlns:xsl="&lt;a href=" http:="" www.w3.org="" 1999="" XSL="" Transform"="" rel="nofollow">http://www.w3.org/1999/XSL/Transform"
    >
<xsl:output method="text"/>

<xsl:template match="/">
<xsl:apply-templates select="Bioseq-set/Bioseq-set_seq-set/Seq-entry"/>
</xsl:template>

<xsl:template match="Seq-entry">
<xsl:value-of select="Seq-entry_seq/Bioseq/Bioseq_id/Seq-id/Seq-id_other/Textseq-id/Textseq-id_accession"/>
<xsl:text>  </xsl:text>
<xsl:for-each select="Seq-entry_seq/Bioseq/Bioseq_annot/Seq-annot/Seq-annot_data/Seq-annot_data_ftable/Seq-feat/Seq-feat_dbxref/Dbtag[Dbtag_db='GeneID']">

<xsl:variable name="geneid" select="Dbtag_tag/Object-id/Object-id_id"/>

<xsl:variable name="url" select="concat('&lt;a href=" http:="" eutils.ncbi.nlm.nih.gov="" entrez="" eutils="" efetch.fcgi?db="gene&amp;retmode=xml&amp;id=',$geneid)" "="" rel="nofollow">http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&retmode=xml&id=',$geneid)"/>

<xsl:value-of select="document($url)/Entrezgene-Set/Entrezgene/Entrezgene_gene/Gene-ref/Gene-ref_locus"/>
<xsl:text>
</xsl:text>
</xsl:for-each>
</xsl:template>

</xsl:stylesheet>

with NCBI efetch/nucleotide:

xsltproc --novalid stylesheet.xsl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=db&retmode=xml&id=NR_045294" 
NR_045294   Gm4285
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

You can download all these annotations from Ensembl http://asia.ensembl.org/biomart/martview/67bf1defc1d2b3e205f0fd5f4506f849

And then use the following command

grep NR_* filename
• 1 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Curiosity • Curiosity

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