We are doing a study analyzing the expression of certain genes and correlating that with response to chemotherapy. So far I have been manually going through every dataset on the NCBI website and teasing out which ones have "therapy response" or any variation of that as a variable. Is there a more efficient way to do this? Like a query to filter out highthroughput/microarray data that also contains therapy response/pathologic complete response/etc. Any help would be greatly appreciated. Thanks.
Hi Norman,
if you used the filters in GEO profiles and found nothing maybe you could go an other way. try in the pubmed query and see in found papers which one has data deposited in GEO...
fred
Hi Norman Fultang ,
There are several ways of GEO queries. You may search with any free text, or with the gene symbols of your interest, gene ontology terms, specific chromosome loci, platform etc.
You may refer this https://www.ncbi.nlm.nih.gov/geo/info/qqtutorial.html for the advanced search options.
Regards
My guess is that because GEO doesn't capture treatment details in easily searchable format, getting this information programmatically isn't going to be easy, although you could probably use the query terms to narrow down your search.
You might be better off using a more specific database, like LINCS (http://www.lincsproject.org/LINCS/about) which focuses specifically on chemical perturbations.
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