Database for finding SNPs (Mutation-deletion/SNPs) In the promotor region of any gene

Question

[vrun.bnsl]

Is there any online database in which I can find the mutations in the promotor region of oncogenes. Cosmic and other databases are not good for that purpose.Any one ???

Answer 1

[David Fredman]

There are many good alternatives. You could use

• Biomart through http://www.ensembl.org to export a list of SNPs in the promoters of genes (attributes) and filter it by your oncogene gene identifiers (if you have such a list, or can generate it).
• The snpEff tool through https://usegalaxy.org is another alternative.
• Ensembl variant effect predictor (There's a web version as well as a download.

If you are also interested in SNPs with potential regulatory effect that are outside of the promoter, you can explore:

• Regulome
• Haploreg

[vrun.bnsl]

Thanks for your response but how to confine the result to promotor region only.Within 1000 bp. Sorry , I am new to bioinformatics. Still not get it.The snpEff tool i guess is only restricited to c.elegans not homo sapiens

[David Fredman]

snpEff can be used with human data, to be sure.

However, if you wish you extract public SNPs that are found within given (custom chosen by you) genomic regions (e.g. within 1000 bp upstream of the transcription start sites of your genes of interest), I suggest you work through tutorials/peruse the documentation and then attempt to use either Biomart (linked to above), UCSC table browser (http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html), or Galaxy (https://usegalaxy.org/).

Answer 2

[Charles Warden]

ANNOVAR annotates disruptions of conserved transcription factor binding sites

http://www.openbioinformatics.org/annovar/

FunSeq gives scores for non-coding variants, but I personally prefer the ANNOVAR report.

http://funseq.gersteinlab.org/