How To Find Samples(Or Datasets) With Overall Survival Time In Geo Or Arrayexpress?
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8.2 years ago
jlshi.nudt ▴ 220

hi, I want to find datasets with overall survival information. But I can custom such a query for GEO or ArrayExpress. Anyone tell me how to custom such a query? thank you.

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Could you further define "overall survival time"? If you are thinking about the time a patient lived after having the sample taken then no, you won't be able to query for that.

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8.2 years ago

I don't think you can directly query the metadata, but you can find such data using two strategies:

1) I think most TCGA cohorts have overall survival data

https://tcga-data.nci.nih.gov/tcga/

2) Look for large patient cohorts in GEO or ArrayExpress and then see what annotations some with the samples.

For example, this breast cancer dataset has overall survival data:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7390

If you click on the first sample you will see:

t.os: 937

e.os: 1

t.os = overall survival time

e.os = overall survival event (i.e. dead or alive --> this particular dataset also has regression free survival).

Sometimes you may have to contact the corresponding author on a paper to interpret the GEO metadata

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Thank you. TCGA is a good data center, but it seems that only little data provides open access.

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For certain things (like DNA variants), I would agree. However, I think the gene expression data (which is most typically used with survival) is actually pretty good. For example, RNA-Seq usually has RPKM values (and you probably don't need the raw data for that).

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