Pulmonary Hypertension Engine for Linked Experiments (PHELEX): a platform for the re-analysis of public transcriptomic data related to pulmonary hypertension in both animal models, and humans.

Abstract

Pulmonary hypertension (PH) is a vasculopathy that results in elevated mean pulmonary arterial pressures over 20mmHg. Despite significant advances in research, PH still has a high mortality rate, and there is currently no cure for the disease. As with all biomedical fields, PH researchers have embraced the power of next generation technologies such as microarrays and RNA sequencing. Most of these data can be found on public repositories, which is usually a requirement for publication. While these repositories are rich sources of data, they require intermediate to advanced bioinformatics skills to access, download, and make these data useful. Here we present Pulmonary Hypertension Engine for Linked Experiments (PHELEX), which represents a comprehensive catalogue of all RNA sequencing data related to PH that is currently available on the Gene Expression Omnibus (GEO), hosted by the US National Centre for Biotechnology Information (NCBI). We identified 2,278 bulk RNA sequencing samples from human, mouse and rat, and built a searchable tool based on the metadata that is associated with each sample. PHELEX is a functional tool that allows selected studies to be highlighted, and parsed through Confidence, an analysis tool we have created, which will model the data based on user-defined classifiers, perform differential gene expression and pathway analysis, and present these data using standard graphics, and text-file results. PHELEX also allows PH researchers to cross-cut between discrete studies, facilitating de novo understanding of these data. As a robust searchable repository of genomic data, we hope that PHELEX will accelerate PH innovation and discovery, by allowing researchers to mine existing genomic data and thus better understand the molecular signatures that underpin PH.