Meta-analysis of public hypoxic transcriptomes for cancer researches

In order to elucidate functional insights in hypoxic response in data-driven way, we have attempted meta-analysis of hypoxic transcriptome for public expression data which have been archived as microarray and RNA-seq data in public transcriptome databases.

While various hypoxic conditions (oxygen concentration and duration of hypoxia) and cell lines are taken in the stored data, we manually curated possible pairs of transcriptome before and after hypoxic stress from microarray and RNA-seq data. The number of experiments for all genes was counted and those were classified into three categories, which are up-regulated, down-regulated, and unchanged. Genes up-regulated in all records contained well-studied hypoxia responsive genes, while down-regulated genes were unfamiliar in hypoxia.

Meta-analysis approach to public gene expression database is useful for selecting candidate genes from gene expression profiles of various experimental conditions. The data produced in this study are open and ready for use to all cancer researchers.