Quantifying Data Sets From Public Repositories

Is there a method (relatively automatic) for quantifying the datasets in ArrayExpress or Gene Expression Omnibus, for example?

I would like to make some statistics on the number of datasets per platform,tissue type,species etc

Otherwise, which would be the best way to do it?

Example

Array Express:

http://www.ebi.ac.uk/arrayexpress/browse.html

I would like to filter experiments from this type of listing and quantify the data sets. 4 datasets chip-seq, mus musculus, 3 datasets rna seq homo sapiens, etc

microarray geo database data

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updated 14.5 years ago by Alastair Kerr

• written 14.5 years ago by Agatha •

1 answer

EDIT I read your question as gene centric rather than database centric. Hence this edit,

GEO has a good summary table you can use: The Summary page has 5 tabs that will give you the summary data based on platform/series/sample/organism but not tissue. I would get in touch with the ncbi help desk for this but the data might be accesible via the sql backend.

Old Answer: This sounds very similar to the data found in BioGPS. Note: check the apps section for increased functionality as well as the downloads section for the underlying data.

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written 14.5 years ago by Alastair Kerr

@Alastair Kerr -I've had a brief look, I will look more carefully. However it seems like you can search for individual genes..I would like to have some statistics on the entire datasets containing expression data stored in the public repositories..like 4 datasets expression data, microarray, small non coding rnas; 2 datasets expression data, microarray, small nc rnas , mus musculus etc

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