Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks - Centre Eugène Marquis Access content directly
Conference Papers Year : 2023

Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks

Abstract

Non-coding RNAs and their biological functions are still incompletely understood, while representing a large part of the human transcriptome and having an important role in cancer. Among these, circular RNAs (circRNAs) have recently been discovered for their microRNA (miRNA) sponge function, which allows them to modulate the expression of miRNA target genes: they take on the role of competitive endogenous RNAs (ceRNAs). Their closed-loop structure makes them highly stable and their miRNA binding capacity seems much more powerful than that of any other ceRNAs, leading to their super-sponge naming. Today, few ceRNA prediction computational tools have been published and most of them do not consider ce-circRNAs. Moreover, the few studies focusing on circRNA-miRNA-mRNA networks have not developed a tool that automates the search for ceRNAs from user's transcriptomic data. In this study, we present an interactive Shiny web application, called Cirscan for CIRcular RNA Sponge CANdidates. Cirscan automatically infers circRNA-miRNA-mRNA networks from human multi-level transcript expression data (including circRNAs, mRNAs, and optionally miRNAs in the case of cancer study) from two biological conditions (e.g. tumor versus normal conditions) in order to identify potential sponge mechanisms, active in a specific condition. Cirscan calculates a global sponge score for each miRNA-circRNA interaction, integrating multiple criteria based on interaction reliability and on RNA expression level using the TOPSIS method. The ranking of this score provides the most relevant circRNA candidates being miRNA sponges. Finally, the user is able to visualize the top ranked sponge mechanisms as graphs, where nodes correspond to the different types of RNAs and edges to the miRNA-target interactions. In order to help the user in the biological interpretation of the visualized network, an enrichment analysis of the biological functions is performed. We applied Cirscan on a public multi-level microarray transcript expression dataset from colorectal cancer (CRC) and retrieved previously described sponge mechanisms as well as novel circRNA sponge candidates.
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Dates and versions

hal-04286509 , version 1 (15-11-2023)

Identifiers

  • HAL Id : hal-04286509 , version 1

Cite

Rose-Marie Fraboulet, Yanis Si Ahmed, Marc Aubry, Sébastien Corre, Marie-Dominique Galibert, et al.. Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks. JOURNÉES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHÉMATIQUES (JOBIM ) 2023, Jun 2023, Diverses villes françaises, France. ⟨hal-04286509⟩
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