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

Question

[Hamilton]

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?

Answer 1

[Pierre Lindenbaum]

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

Answer 2

[Curiosity]

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

And then use the following command

grep NR_* filename