Rna-Seq Datasets For Co-Expression Network Benchmark

Question

[Alan R. Fachini]

Hi guys. When working with image classification, it is common to have a benchmark datasets used by all research papers to test new algorithms and hypothesis. I would like to know if there are common RNA-seq datasets out there used for co-expression network analysis and where I could find them. I.e.: A dataset should have the RNA-seq data in an open format and the expected network (validated by biologists). We them can use this dataset to test new algorithms (like changing the correlation function) and see if they return the expected result or use metrics to see how close the result is to the expected network. I am also interested in competitions (if some exists) that use this data to test new algorithms. Thanks!

Answer 1

[Alan R. Fachini]

Maybe I can use the Gene Expression Omnibus for this. What are others using?

"GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles."