AUTHOR=Freiesleben Sherry , Unverricht-Yeboah Marcus , Gütebier Lea , Waltemath Dagmar , Kriehuber Ralf , Wolkenhauer Olaf TITLE=A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools JOURNAL=Frontiers in Systems Biology VOLUME=2 YEAR=2022 URL=https://www.frontiersin.org/journals/systems-biology/articles/10.3389/fsysb.2022.928159 DOI=10.3389/fsysb.2022.928159 ISSN=2674-0702 ABSTRACT=
MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are involved in the modulation of the DNA-damage response (DDR) and upon exposure to ionizing radiation (IR), their expression fluctuates. In this study, we propose a workflow that enables the creation of regulatory networks by integrating transcriptomics data as well as regulatory data in order to better understand the interplay between genes, transcription factors (TFs), miRNAs, and lncRNAs in the cellular response to IR. We preprocessed and analyzed publicly available gene expression profiles and then applied our consensus and integration approach using open source data and tools. To exemplify the benefits of our proposed workflow, we identified a total of 32 differentially expressed transcripts corresponding to 20 unique differentially expressed genes (DEGs) and using these DEGs, we constructed a regulatory network consisting of 106 interactions and 100 nodes (11 DEGs, 78 miRNAs, 1 DEG acting as a TF, and 10 lncRNAs). Overrepresentation analyses (ORAs) furthermore linked our DEGs and miRNAs to annotations pertaining to the DDR and to IR. Our results show that