Mapping Features From Cdna To Gene

Question

[Curly]

Hello,

I have a batch of possible snps that I've marked in terms of base position against a NCBI refseq sequence (some of these SNP's aren't available in a public resource - so no rsID's as yet). I would like to display/plot these against the gene for that refseq cdna - perhaps in ensembl. Is this possible? I also tried using GeneomeGraphs in Bioconductor - but had problems with the intervening intron sequences - as each intron caused the base coordinates to change eg hypothetically, base 1 on refseq maps to base 1 on gene but base 50 on refseq may map to base 300 on gene as there is an intron in between! Further introns lead to more coordinate shifting.

Many thanks.

Answer 1

[Prateek]

My first suggestion would be to get the absolute chromosome coordinates of each of the SNPs. Then you'll have one language of coordinates across CDNAs, transcripts exons, introns etc.[?]

To do this, you can get the refgene.txt.tgz file from here[?] http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/[?][?] This file has all refseq ids with their chromosome coordinates along with CDS start/end, exon start/end, strand etc. [?]for column descriptions, see refgene.sql file in the same location. [?] Once you have converted to chr coords, you from now on use ensemble biomart to get all your gene/CDS coordinates and plot your SNPs along them.

1. go to ensemble biomart http://uswest.ensembl.org/biomart/martview
2. choose ensemble genes 60 and then Homosapiens genes
3. set attributes on left column to obtain your results.

[Curly]

Many thanks for your help Prateek!

Answer 2

[Giulietta - Ensembl Helpdesk]

Ensembl allows you to enter your own variations and either determine which Ensembl transcript they fall in, or plot them against the genome (in which case you can turn on RefSeq cDNAs to view them together, along the genome.) Here is the 'variant effect predictor' tool and an example of input/output- you do need genomic coordinates, as the above answer pointed out.

http://www.ensembl.org/tools.html (online version or API script)

http://www.ensembl.org/info/website/upload/var.html

Alternatively, go to Region in Detail (the Location tab).

For example: http://www.ensembl.org/Homo_sapiens/Location/View?r=6:133017695-133161157

Click 'Manage your data' at the left.

You can attach a file or url, with genomic coordinates for your SNPs. Once you upload it, you can view it on the Region in Detail page. To more clearly see the Human (in this case) RefSeq/EMBL track, go to 'configure this page' and change the track setting to 'labels' or 'normal'. You can always export a pic using the 'Export image' button at the lower right of the panel.

More info about upload formats:

http://www.ensembl.org/info/website/upload/index.html

If you would like more help, email us (Ensembl) at [e-mail]