Data mining for 300 genes from GEO

Question

[GR]

Hi All,

I have a gene list of ~ 300 genes. I want to get from GEO all the high-throughput expression studies for these genes. I can write a R script to make this search with GEOsearch package. But I guess the package only allows for geneid/name based search. I was wondering if there is a way to search based on advanced options, e.g. get only expression data where the sample source is root.

Answer 1

[theobroma22]

I think you could a local Blastx program on the 300 amino acid sequences, and parse the gene IDs to a list to use with your GEOsearch.