Differentially expressed genes data sets for download

Question

[Mk]

Hi,

I want to download some publicly available differential gene expression datasets for my work. Not sure where to start with and it will be great to get some tips on where to look for.

I checked the GEO for datasets and found files in soft format, but I am looking for files in tab-delimited ASCII text format (similar to the ones used for GSEA)

[Benn]

Try starting with formulating a research question first.

Answer 1

[Istvan Albert]

Downloading the differential expression data (AKA the actual research finding of a paper) usually turns out to be surprisingly convoluted. It shows the sorry state of the bioinformatics data distribution.

The SOFT files are in fact, ASCII text and tabular format, but you will need to do some parsing to make sense of (drop the initial header lines at the very least). That being said SOFT files represent measures and will not contain other all information that is typically used in a differential expression study.

Data tables with fold changes, p-values, corrected p-values etc are usually only available in the supplementary information published with the paper, usually will be non-standardized, interpreting them requires some manual intervention.