Next Article in Journal
Interleukin Gene Variability and Periodontal Bacteria in Patients with Generalized Aggressive Form of Periodontitis
Next Article in Special Issue
Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study
Previous Article in Journal
Clinical Assessment, Genetics, and Treatment Approaches in Autism Spectrum Disorder (ASD)
Previous Article in Special Issue
In-silico Analysis of NF1 Missense Variants in ClinVar: Translating Variant Predictions into Variant Interpretation and Classification
Article

Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies

1
Chair of Medical Informatics, Friedrich-Alexander University (FAU) of Erlangen-Nürnberg, 91058 Erlangen, Germany
2
Functional Genomics and Systems Biology Group, Department of Bioinformatics, University of Würzburg, 97074 Würzburg, Germany
3
Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, 30625 Hannover, Germany
4
Medical Center for Information and Communication Technology, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
5
National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK
6
Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
7
Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
8
REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2020, 21(13), 4727; https://doi.org/10.3390/ijms21134727
Received: 9 June 2020 / Revised: 27 June 2020 / Accepted: 28 June 2020 / Published: 2 July 2020
(This article belongs to the Special Issue In Silico Analyses: Translating and Making Sense of Omics Data)
Integrative bioinformatics is an emerging field in the big data era, offering a steadily increasing number of algorithms and analysis tools. However, for researchers in experimental life sciences it is often difficult to follow and properly apply the bioinformatical methods in order to unravel the complexity and systemic effects of omics data. Here, we present an integrative bioinformatics pipeline to decipher crucial biological insights from global transcriptome profiling data to validate innovative therapeutics. It is available as a web application for an interactive and simplified analysis without the need for programming skills or deep bioinformatics background. The approach was applied to an ex vivo cardiac model treated with natural anti-fibrotic compounds and we obtained new mechanistic insights into their anti-fibrotic action and molecular interplay with miRNAs in cardiac fibrosis. Several gene pathways associated with proliferation, extracellular matrix processes and wound healing were altered, and we could identify micro (mi) RNA-21-5p and miRNA-223-3p as key molecular components related to the anti-fibrotic treatment. Importantly, our pipeline is not restricted to a specific cell type or disease and can be broadly applied to better understand the unprecedented level of complexity in big data research. View Full-Text
Keywords: big data; transcriptomics; integrative bioinformatics; algorithm; web application; natural compounds; miRNAs; cardiac fibrosis big data; transcriptomics; integrative bioinformatics; algorithm; web application; natural compounds; miRNAs; cardiac fibrosis
Show Figures

Figure 1

MDPI and ACS Style

Fuchs, M.; Kreutzer, F.P.; Kapsner, L.A.; Mitzka, S.; Just, A.; Perbellini, F.; Terracciano, C.M.; Xiao, K.; Geffers, R.; Bogdan, C.; Prokosch, H.-U.; Fiedler, J.; Thum, T.; Kunz, M. Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies. Int. J. Mol. Sci. 2020, 21, 4727. https://doi.org/10.3390/ijms21134727

AMA Style

Fuchs M, Kreutzer FP, Kapsner LA, Mitzka S, Just A, Perbellini F, Terracciano CM, Xiao K, Geffers R, Bogdan C, Prokosch H-U, Fiedler J, Thum T, Kunz M. Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies. International Journal of Molecular Sciences. 2020; 21(13):4727. https://doi.org/10.3390/ijms21134727

Chicago/Turabian Style

Fuchs, Maximilian, Fabian P. Kreutzer, Lorenz A. Kapsner, Saskia Mitzka, Annette Just, Filippo Perbellini, Cesare M. Terracciano, Ke Xiao, Robert Geffers, Christian Bogdan, Hans-Ulrich Prokosch, Jan Fiedler, Thomas Thum, and Meik Kunz. 2020. "Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies" International Journal of Molecular Sciences 21, no. 13: 4727. https://doi.org/10.3390/ijms21134727

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop