Original title: Co-expression analysis of small RNAs and untranslated regions in Rhodospirillum rubrum
Authors: Heřmánková, Kristýna ; Sedlář, Karel
Document type: Papers
Language: eng
Publisher: Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií
Abstract: Bacterial small RNAs (sRNAs) are regulatory elements often mentioned in the context of stress response. So are polyhydroxyalkanoates (PHAs), a possible replacement for conventional plastics, are frequently produced by bacteria facing stress conditions. PHAs then serve as the source of the carbon as well as the defense mechanism against further stress. Here, we present sRNA analysis of PHA-producing bacterium Rhodospirillum rubrum, especially the co-expression analysis of inferred sRNA candidates from RNA-Seq data. Weighted correlation network analysis (WGCNA) was used to compute clusters of genes with similar expression profiles, resulting in 28 modules. Further, the functional annotation of genes in each module was applied and the overall functional profiles were mentioned using a ‘guilt by association’ approach. Additionally, functional enrichment of modules was obtained through overrepresentation analysis (ORA). These results provide an overview of regulatory elements and their predicted functions in R. rubrum, which further unveil its dynamic properties and can help with the assessment of its industrial application.
Keywords: coexpression analysis; functional annotation; PHA; RNA-Seq; sRNA
Host item entry: Proceedings I of the 30st Conference STUDENT EEICT 2024: General papers, ISBN 978-80-214-6231-1, ISSN 2788-1334

Institution: Brno University of Technology (web)
Document availability information: Fulltext is available in the Brno University of Technology Digital Library.
Original record: https://hdl.handle.net/11012/249209

Permalink: http://www.nusl.cz/ntk/nusl-622519


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