L’ARN circulaire nous joue-t-il des tours ?

Lacazette, Éric; Diallo, Leila; Tatin, Florence; Garmy‐Susini, Barbara; Prats, Anne-Catherine

doi:10.1051/medsci/2019267

Cited by 4 publications

(1 citation statement)

References 33 publications

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“…Advances in sequencing technologies have led to the identification of different types of ncRNAs in the cell, such as long non-coding RNAs and microRNAs (miRNAs) [ 2 ]. In this study, we are interested in circular RNAs (circRNAs), a category of recently discovered ncRNAs known for their miRNA sponge function [ 3 , 4 ]. MicroRNAs typically bind to mRNA through miRNA Recognition Elements (MREs), resulting in the degradation of their mRNA targets.…”

Section: Introductionmentioning

confidence: 99%

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

Fraboulet,

Si Ahmed,

Aubry

et al. 2024

BMC Bioinformatics

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Background Non-coding RNAs represent a large part of the human transcriptome and have been shown to play an important role in disease such as cancer. However, their biological functions are still incompletely understood. Among non-coding RNAs, circular RNAs (circRNAs) have recently been identified for their microRNA (miRNA) sponge function which allows them to modulate the expression of miRNA target genes by taking on the role of competitive endogenous RNAs (ce-circRNAs). Today, most computational tools are not adapted to the search for ce-circRNAs or have not been developed for the search for ce-circRNAs from user’s transcriptomic data. Results In this study, we present Cirscan (CIRcular RNA Sponge CANdidates), an interactive Shiny application that automatically infers circRNA–miRNA–mRNA networks from human multi-level transcript expression data from two biological conditions (e.g. tumor versus normal conditions in the case of cancer study) in order to identify on a large scale, potential sponge mechanisms active in a specific condition. Cirscan ranks each circRNA–miRNA–mRNA subnetwork according to a sponge score that integrates multiple criteria based on interaction reliability and expression level. Finally, the top ranked sponge mechanisms can be visualized as networks and an enrichment analysis is performed to help its biological interpretation. We showed on two real case studies that Cirscan is capable of retrieving sponge mechanisms previously described, as well as identifying potential novel circRNA sponge candidates. Conclusions Cirscan can be considered as a companion tool for biologists, facilitating their ability to prioritize sponge mechanisms for experimental validations and identifying potential therapeutic targets. Cirscan is implemented in R, released under the license GPL-3 and accessible on GitLab (https://gitlab.com/geobioinfo/cirscan_Rshiny). The scripts used in this paper are also provided on Gitlab (https://gitlab.com/geobioinfo/cirscan_paper).

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Section: Introductionmentioning

confidence: 99%

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

Fraboulet,

Si Ahmed,

Aubry

et al. 2024

BMC Bioinformatics

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Quel cirque, ces virus

2023

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Les ARN circulaires (ARNcirc) font partie intégrante de la relation hôte-pathogène. Après la description de la dérégulation d’ARNcirc cellulaires lors d’infections virales, de nombreux ARNcirc d’origine virale ont été identifiés et caractérisés. Des rôles régulateurs, aussi bien du cycle cellulaire que du cycle viral, leur ont été attribués. Ils sont associés à l’oncogenèse viro-induite, à la régulation du système immunitaire et à la différenciation cellulaire. Ces boucles d’ARN, aussi archaïques que les premiers virus, réservent bien des surprises aux chercheurs tant au niveau de leurs fonctions que de leurs biogenèses !

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

Fraboulet,

Ahmed,

Aubry

et al. 2023

Preprint

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BackgroundNon-coding RNAs represent a large part of the human transcriptome and have been shown to play an important role in disease such as cancer. However, their biological functions are still incompletely understood. Among noncoding RNAs, circular RNAs (circRNAs) have recently been identified for their microRNA (miRNA) sponge function which allows them to modulate the expression of miRNA target genes by taking on the role of competitive endogenous RNAs (ce-circRNAs). Today, most computational tools are not adapted to the search for ce-circRNAs or have not been developed for the search for ce-circRNAs from user’s transcriptomic data.ResultsIn this study, we present Cirscan (CIRcular RNA Sponge CANdidates), an interactive Shiny application that automatically infers circRNA-miRNA-mRNA networks from human multi-level transcript expression data from two biological conditions (e.g. tumor versus normal conditions in the case of cancer study) in order to identify on a large scale, potential sponge mechanisms active in a specific condition. Cirscan ranks each circRNA-miRNA-mRNA subnetwork according to a sponge score that integrates multiple criteria based on interaction reliability and expression level. Finally, the top ranked sponge mechanisms can be visualized as networks and an enrichment analysis is performed to help its biological interpretation. We showed on two real case studies that Cirscan is capable of retrieving sponge mechanisms previously described, as well as identifying potential novel circRNA sponge candidates.ConclusionsCirscan can be considered as a companion tool for biologists, facilitating their ability to prioritize sponge mechanisms for experimental validations and identifying potential therapeutic targets. Cirscan is implemented in R, released under the license GPL-3 and accessible on GitLab (https://gitlab.com/geobioinfo/cirscan_Rshiny). The scripts used in this paper are also provided on Gitlab (https://gitlab.com/geobioinfo/cirscan_paper).

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L’ARN circulaire nous joue-t-il des tours ?

Cited by 4 publications

References 33 publications

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

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

Quel cirque, ces virus

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

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