Retrieve Ensembl Gene Ids From List Of Regions Using Hg18 Annotation

Question

[Rubal7]

Hello Everyone,

I have regions lists in text files in the formate taken by Ensembl Biomart, eg: 10:55500000:55999999:1 10:55500000:55999999:-1 4:158500000:158999999:1 4:158500000:158999999:-1 5:120500000:120999999:1 5:120500000:120999999:-1 9:104500000:104999999:1 9:104500000:104999999:-1 22:48000000:48499999:1 22:48000000:48499999:-1

I have been using these lists with Ensembl Biomart to get the lists of genes within these regions as output text files. However Biomart appears to use the latest HG19 annotation (makes sense), and now I would like to do the same with regions that are mapped to HG18. Is there a way to select HG18 annotation on biomart, or is there another tool that can take this input and give me HG18 gene annotations? I am considering liftingover these regions to HG19, then presumably I could use Biomart with the HG19 annotations, but as the analyses are based on HG18 I think it is inconsistent to then use HG19 gene annotations. Ideally there will be a way to select HG18 annotations in biomart.

If anyone has any experience with this your help is greatly appreciated. Thank you in advance.

Best,

Rubal

Answer 1

[VS]

Just google -- your answer is the first hit. In the Bioconductor mailing list here : https://stat.ethz.ch/pipermail/bioconductor/2010-March/032487.html

listMarts(host="may2009.archive.ensembl.org", path="/biomart/martservice",archive=FALSE)

[Rubal7]

thanks for pointing me to that

Answer 2

[Obi Griffith]

The answer from VS explains how you would do this in R with the biomaRt library. If you were hoping to use the web interface this is also still available through Ensembl's archive site here: http://may2009.archive.ensembl.org/biomart/martview/

For future reference you can find this by going to Ensembl, choosing Human, View in Archive Site, select the last remaining Ensembl archive which corresponds to hg18 (NCBI36), and then follow the BioMart link for this archive version of Ensembl.

[Rubal7]

thanks that's great