RT journal article
T1 Exploring miRNA–target gene pair detection in disease with coRmiT
A1 Córdoba Caballero, José
A1 Perkins, J. R.
A1 García Criado, Federico
A1 Gallego, Diana
A1 Navarro Sánchez, Alicia
A1 Moreno Estellés, Mireia
A1 Garcés, Concepción
A1 Bonet Martínez, Fernando
A1 Romá-Mateo, Carlos
A1 Toro Cebada, Rocío
A1 Perez, Belén
A1 Sanz, Pascual
A1 Koh, Matthias
A1 Rojano, Elena
A1 Seoane, Pedro
A1 Ranea, Juan A.G.
A2 Medicina
K1 miRNA
K1 RNA-Seq
K1 correlation
K1 odds ratio
K1 genetic disease
K1 target
AB A wide range of approaches can be used to detect micro RNA (miRNA)–target gene pairs (mTPs) from expression data, differing inthe ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus onwhich is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinctrare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related tothe disease pathology. All datasets were preprocessed using a standardized, freely available computational workf low, DEG_workf low.This workf low includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of thedetected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTPdetection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the onewith the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration methodto the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have importantimplications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.
PB Oxford
SN 1477-4054
YR 2024
FD 2024-01-10
LK http://hdl.handle.net/10498/32814
UL http://hdl.handle.net/10498/32814
LA eng
DS Repositorio Institucional de la Universidad de Cádiz
RD 08-nov-2026