Functional Organization of Public Gene Expression Data

In order to promote life science researches in Japan, we have made databases easier to use under the integrated database project in Japan.

Sequence Read Archive(SRA) stores raw sequencing data and alignment information from high-throughput sequencing platforms, and it currently contains thousands of RNA-seq data from transcriptome sequencing. But transcriptome data from microarray is still the majority of data in public gene expression databases known as NCBI Gene Expression Omnibus (GEO) and EBI ArrayExpress. 

It is not easy to draw new discoveries by comparing datasets from those transcriptomes because of the complexity of relationships among those databases.As a part of the integrated database project in Japan, we are developing the yellow pages for publicly available gene expression data, called AOE (All Of gene Expression; http://aoe.dbcls.jp/).

Concurrently, we have developed reference gene expression data set of mammalian tissues and cell lines measured by different types of methods (EST, GeneChip, CAGE and RNA-seq). The data set, which is called RefEx, is archived with user-friendly web interface (http://refex.dbcls.jp/) in addition to bulk download of the whole data set. RefEx now integrates gene expression data (hundreds of cell lines, primary cells, adult and fetal tissues  in human and mouse) by FANTOM5 CAGE to be re-used in comparative transcriptomics.

AOE and RefEx is freely available without registration.