recurrent pathway in a list of gene from SNP array

Question

[yannick.lebris]

Hello,

I have 2 questions :

I have datas from SNP array( affymetrix) tested on a serie of tumors samples.

• How can I generate a list of gene from each chromosomic region altered (example : chr1:55397406-120508803(1p32:3-1p12)). I have a list of 68 regions and I need to list genes of each region.

• With this list of gene, which open sofware can I use to evaluate the recurrent pathway implicated?

Thank you for help.

YLB

Answer 1

[Denise CS]

Answer for question a) is BioMart. Use your list of chromosomal locations (or cytogenetic bands) and get the genes annotated in that region. Please bear in mind, some of your regions may retrieve no genes at all. There can be a SNP there (e.g. downstream_gene_variant), but no gene. Once you get your list of genes, you can search for their pathways using Reactome to answer question b).