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bioRxiv · 10.1101/2022.07.30.502025

Magnetique: An interactive web application to explore transcriptome signatures of heart failure

Britto-Borges, T.·Ludt, A.·Boileau, E.·Gjerga, E.·Marini, F.·Dieterich, C.
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Abstract

Despite a recent increase in the number of RNA-seq datasets investigating heart failure (HF), accessibility and usability remain critical issues for medical researchers. We present Magnetique (https://shiny.dieterichlab.org/app/magnetique), an interactive web application to explore the transcriptional signatures of heart failure. We reanalyzed the Myocardial Applied Genomics Network RNA-seq dataset, one of the largest publicly available datasets of left ventricular RNA-seq samples from patients with dilated (DCM) or hypertrophic (HCM) cardiomyopathy, as well as unmatched non-failing hearts from organ donors and patient characteristics that allowed us to model confounding factors. Focusing on the DCM versus HCM contrast, we identified 201 differentially expressed genes and associated pathway signatures. Moreover, we predict underlying signaling networks based on inferred transcription factor activities. To the best of our knowledge, Magnetique is the first online application to provide an interactive view of the HF transcriptome by analyzing differential transcript isoform usage. Finally, another graphical view on statistically predicted RNA-binding protein to target transcript interactions complements the Magnetique web application. The source code for both the analyses (https://github.com/dieterich-lab/magnetiqueCode2022) and the web application (https://github.com/AnnekathrinSilvia/magnetique) is available to the public. We hope that our application will help users to uncover the molecular basis of heart failure.

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Britto-Borges, T., Ludt, A., Boileau, E., Gjerga, E., Marini, F., Dieterich, C.. 2022-08-02. Magnetique: An interactive web application to explore transcriptome signatures of heart failure. https://doi.org/10.1101/2022.07.30.502025

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