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. 2020 Jan 24;15(1):e0227076.
doi: 10.1371/journal.pone.0227076. eCollection 2020.

All of gene expression (AOE): An integrated index for public gene expression databases

Hidemasa Bono  1
Affiliations

All of gene expression (AOE): An integrated index for public gene expression databases

Hidemasa Bono. PLoS One. .

Abstract

Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA). We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE. AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Comparison of EBI ArrayExpress and NCBI Gene Expression Omnibus.
The number of overlapping data-series entries in ArrayExpress (left) and Gene Expression Omnibus (right).
Fig 2
Fig 2. How to make AOE index.
Three levels of AOE data flow are required to make the AOE index. Level 1 from ArrayExpress data, level 2 from GEO data in SRA via DBCLS SRA API, and level 3 from RNA-seq data in SRA, but not in GEO via DBCLS SRA API.
Fig 3
Fig 3. AOE web interface.
Users can retrieve data of interest graphically in the AOE web interface.
See this image and copyright information in PMC

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