TY - JOUR T1 - Meta-analysis of hypoxic transcriptomes from public databases JF - bioRxiv DO - 10.1101/267310 SP - 267310 AU - Hidemasa Bono AU - Kiichi Hirota Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/12/03/267310.abstract N2 - Hypoxia is the insufficiency of oxygen in the cell, and hypoxia-inducible factors (HIFs) are central regulators of oxygen homeostasis. In order to obtain functional insights into the hypoxic response in a data-driven way, we attempted meta-analysis of the RNA-seq data from the hypoxic transcriptome archived in public databases. In view of methodological variability, we first manually curated RNA-seq data from appropriate pairs of transcriptomes before and after hypoxic stress. These included 128 human and 52 murine transcriptome pairs. We classified the results of experiments for each gene into three categories: upregulated, downregulated, and unchanged. Hypoxic transcriptomes were then compared between humans and mice to identify common hypoxia-responsive genes. In addition, meta-analyzed hypoxic transcriptome data were integrated with public ChIP-seq data on the known human HIFs HIF1A and EPAS1 in order to provide insights into hypoxia-responsive pathways involving direct transcription factor binding. This study provides a useful resource for hypoxia research. It also demonstrates the potential of a meta-analysis approach to public gene expression databases for selecting candidate genes from gene expression profiles generated under various experimental conditions. ER -