The Digital Expression Explorer

The Digital Expression Explorer (DEE) is a repository of digital gene expression profiles mined from public RNA-seq data sets. These data are obtained from NCBI Short Read Archive.

Users please note

Due to the El-Osta lab relocation to Monash Central Clinical school at the end of 2016, this resource will likely disappear some time in 2017. We are working on a new version of DEE that will host more data and more features, which will appear in 2017.

Hosted RNA-seq data

Species Datasets Updated
Arabidopsis thaliana 14269 2016-11-11
Caenorhabditis elegans 4105 2016-11-11
Drosophila melanogaster 14124 2016-11-11
Danio rerio 13413 2016-11-12
Escherichia coli 2135 2016-11-12
Homo sapiens 95517 2016-11-13
Mus musculus 127082 2016-11-15
Rattus norvegicus 6893 2016-11-12
Saccharomyces cerevisiae 7055 2016-11-12

Select an organism of interest

Arabidopsis thaliana
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Escherichia coli
Homo sapiens
Mus musculus
Rattus norvegicus
Saccharomyces cerevisiae

Search for data sets of interest

Search accession numbers Multiple accessions can be separated by commas.
Try GSE44682,SRP038903,SRX704261,SRR1578746 for C. elegans.

Search for keywords Case-insensitive single word search.
Try "pathogen" for E. coli.

More sophisticated keyword searches can be done at GEO and SRA, to identify studies and accession numbers of interest.

Keyword searches in mouse and human take up to a minute to complete.


Although all reasonable efforts have been taken to ensure the accuracy and reliability of the data, Baker IDI do not and cannot warrant the performance or results that may be obtained by using this software or data. Baker IDI disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.


Ziemann M, Kaspi A, Lazarus R, El-Osta A. Digital Expression Explorer: A user-friendly repository of uniformly processed RNA-seq data. ComBio2015 DOI: 10.13140/RG.2.1.1707.5926 See our poster

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