circGPAcorr: an integrative tool for functional annotation of circular RNAs using expression data

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21230%2F25%3A00384573" target="_blank" >RIV/68407700:21230/25:00384573 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00023736:_____/25:00013808

Výsledek na webu

<a href="https://doi.org/10.1186/s13040-025-00468-3" target="_blank" >https://doi.org/10.1186/s13040-025-00468-3</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13040-025-00468-3" target="_blank" >10.1186/s13040-025-00468-3</a>

Jazyk výsledku

angličtina

Název v původním jazyce

circGPAcorr: an integrative tool for functional annotation of circular RNAs using expression data

Popis výsledku v původním jazyce

Circular RNAs play a crucial role in cell development and serve as biomarkers in many diseases. Nevertheless, the function of many circular RNAs remains unknown. This function can be inferred from sponging and silencing interactions with micro RNAs and messenger RNAs. We recently proposed a network-based circRNA functional annotation tool, circGPA. However, validation data for RNA interactions are often sparse and predicted interactions contain many false positives. To address this issue, we propose an extended algorithm named circGPAcorr, which uses expression data to weight the interactions, resulting in more precise functional annotation. To assess the significance of the results, the p-value is calculated using reduction to circGPA, a generating-polynomial-based method. We show that the problem is #P-hard, and thus computationally difficult. The circGPAcorr algorithm is tested on publicly available myelodysplastic syndromes expression data, providing gene ontology annotations that align with the literature on myelodysplastic syndromes. At the same time, we demonstrate its performance in the circRNA-disease annotation task.

Název v anglickém jazyce

circGPAcorr: an integrative tool for functional annotation of circular RNAs using expression data

Popis výsledku anglicky

Circular RNAs play a crucial role in cell development and serve as biomarkers in many diseases. Nevertheless, the function of many circular RNAs remains unknown. This function can be inferred from sponging and silencing interactions with micro RNAs and messenger RNAs. We recently proposed a network-based circRNA functional annotation tool, circGPA. However, validation data for RNA interactions are often sparse and predicted interactions contain many false positives. To address this issue, we propose an extended algorithm named circGPAcorr, which uses expression data to weight the interactions, resulting in more precise functional annotation. To assess the significance of the results, the p-value is calculated using reduction to circGPA, a generating-polynomial-based method. We show that the problem is #P-hard, and thus computationally difficult. The circGPAcorr algorithm is tested on publicly available myelodysplastic syndromes expression data, providing gene ontology annotations that align with the literature on myelodysplastic syndromes. At the same time, we demonstrate its performance in the circRNA-disease annotation task.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/NU20-03-00412" target="_blank" >NU20-03-00412: Role transpozibilních elementů a PIWI-interagujících RNA u myelodysplastického syndromu a jejich možné klinické využití</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

BioData Mining

ISSN

1756-0381

e-ISSN

—

Svazek periodika

18

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

32

Strana od-do

—

Kód UT WoS článku

001541752600001

EID výsledku v databázi Scopus

2-s2.0-105012398662