Abstract
In the last decade, miRNAs have attracted noticeable interest as potential biomarkers of neuropsychiatric conditions. However, a standard methodology for miRNA-Seq analysis does not yet exist, raising concerns about the reproducibility of the in-silico results and limiting their usefulness. This situation motivated us to design a miRNA-Seq pipeline specialized in the analysis of neuropsychiatric data, aiming to integrate the results of several bioinformatics tools in a highly reproducible workflow. In this study, we performed an initial test of the usefulness of our new pipeline, named myBrain-Seq, by reanalyzing four recent miRNA-Seq studies of neuropsychiatric conditions. We then compared the myBrain-Seq results with the original results and with an additional reanalysis done with another pipeline in order to make an estimation of the overall replicability. We found one of the three myBrain-Seq methodologies to be the one with best replicability, although the heterogeneity of the results and the absence of an experimental validation limits our conclusions. Further work is required to assess myBrain-Seq’ performance using a bigger dataset of studies with experimental validation data available.
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Acknowledgements
This study was partially supported by: (i) Instituto de Salud Carlos III through the project PI18/01311 (co-funded by European Regional Development Fund, “A way to make Europe”) to R.C. Agís-Balboa, and (ii) Consellería de Educación, Universidades e Formación Professional (Xunta de Galicia) under the scope of the strategic funding ED431C2018/55-GRC Competitive Reference Group. H. López-Fernández is supported by a “María Zambrano” post-doctoral contract from Ministerio de Universidades (Gobierno de España). D. Pérez-Rodríguez is supported by an “Investigo program” predoctoral contract from Xunta de Galicia.
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Pérez-Rodríguez, D., Pérez-Rodríguez, M., Agís-Balboa, R.C., López-Fernández, H. (2023). Towards a Flexible and Portable Workflow for Analyzing miRNA-Seq Neuropsychiatric Data: An Initial Replicability Assessment. In: Fdez-Riverola, F., Rocha, M., Mohamad, M.S., Caraiman, S., Gil-González, A.B. (eds) Practical Applications of Computational Biology and Bioinformatics, 16th International Conference (PACBB 2022). PACBB 2022. Lecture Notes in Networks and Systems, vol 553. Springer, Cham. https://doi.org/10.1007/978-3-031-17024-9_4
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