Computational Methods and Software Tools for Functional Analysis of miRNA Data

García-Moreno, Adrián; Carmona-Sáez, Pedro

doi:10.3390/biom10091252

Cited by 12 publications

(6 citation statements)

References 84 publications

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“…The first goal was to identify targets of miRNAs dysregulated in RCD2. For this purpose, we have used a similar approach to that described by Garcia-Moreno et al [ 16 ], performing an enrichment analysis of the targets of all 15 miRNAs resulting from the findings reported above ( Figure 3 and Table 1 ) using the database miRDB ( (accessed on 4 January 2022)). We considered all the significant miRNAs in order not to lose important information for the subsequent steps to define the affected pathways.…”

Section: Resultsmentioning

confidence: 99%

Circulating microRNAs Suggest Networks Associated with Biological Functions in Aggressive Refractory Type 2 Celiac Disease

et al. 2022

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Despite following a gluten-free diet, which is currently the only effective therapy for celiac disease, about 5% of patients can develop serious complications, which in the case of refractory type 2 could evolve towards intestinal lymphoma. In this study, we have identified a set of 15 microRNAs in serum discriminating between the two types of refractory disease. Upregulated miR-770-5p, miR-181b-2-3p, miR-1193, and miR-1226-3p could be useful for the better stratification of patients and the monitoring of disease development, while miR-490-3p was found to be dysregulated in patients with refractory type 1. Finally, by using bioinformatic tools applied to the analysis of the targets of dysregulated microRNAs, we have completed a more precise assessment of their functions. These mainly include the pathway of response to Transforming Growth Factor β cell–cell signaling by Wnt; epigenetic regulation, especially novel networks associated with transcriptional and post-transcriptional alterations; and the well-known inflammatory profiles.

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Section: Resultsmentioning

confidence: 99%

Circulating microRNAs Suggest Networks Associated with Biological Functions in Aggressive Refractory Type 2 Celiac Disease

et al. 2022

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“…This suggests that Fisher’s exact test does not present enough robustness for miRNA functional enrichment analyses, even when the bias from miRNA prediction algorithms is eliminated through the utilization of experimentally validated miRNA targets. Despite its drawbacks, however, the standard method is still very popular in published studies [7].…”

Section: Discussionmentioning

confidence: 99%

Bias in miRNA enrichment analysis related to gene functional annotations

Zagganas

Γεωργακίλας

Vergoulis

et al. 2021

Preprint

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Motivation: miRNA functional enrichment is a type of analysis that is used to predict which biological functions may be affected by a group of miRNAs or validate whether a list of dysreg- ulated miRNAs are linked to a diseased state. The standard method for functional enrichment analysis uses the hypergeometric distribution to produce p-values, depicting the strength of the association between a group of miRNAs and a biological function. However, in 2015, it was shown that this approach suffers from a bias related to miRNA targets produced by target prediction algorithms and a new randomization test was proposed. Results: In this paper, we demonstrate the existence of another underlying bias which affects gene annotation data sets; additionally, we show that the statistical measure used for the estab- lished randomization test is not sensitive enough to account for it. For this reason, we propose the use of an alternative statistical measure, the "two-sided overlap", and we show that it is able to alleviate the aforementioned issue. Finally, we develop BUFET2, a miRNA enrichment analysis tool that leverages this measure (along with the old one); it is based on BUFET, a fast and scalable implementation of the established randomization test. Availability and Implementation: BUFET2 is written in C++ and is packaged with a Python wrapper script that facilitates experiment execution. Moreover, BUFET2 also comes pre-packaged in a Linux Docker image published on Docker Hub, thus eliminating the need for code compilation. Finally, BUFET2 is also publicly available to execute through a REST API. All datasets used in the experiments throught this paper are openly accessible on Zenodo (https://doi.org/10.5281/zenodo.5175819).

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“…There are different strategies to analyze miRNA functions by predicting miRNA target genes or using miRNA annotations databases [169]. The most used is by predicting the target genes of the selected miRNAs and performing enrichment analysis through statistical tests (e.g., hypergeometric or Fisher's exact tests).…”

Section: Functional Enrichment Analysis and Microrna-disease Associat...mentioning

confidence: 99%

Hepatitis B Virus and microRNAs: A Bioinformatics Approach

Zulian,

Fiscon,

Paci

et al. 2023

IJMS

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In recent decades, microRNAs (miRNAs) have emerged as key regulators of gene expression, and the identification of viral miRNAs (v-miRNAs) within some viruses, including hepatitis B virus (HBV), has attracted significant attention. HBV infections often progress to chronic states (CHB) and may induce fibrosis/cirrhosis and hepatocellular carcinoma (HCC). The presence of HBV can dysregulate host miRNA expression, influencing several biological pathways, such as apoptosis, innate and immune response, viral replication, and pathogenesis. Consequently, miRNAs are considered a promising biomarker for diagnostic, prognostic, and treatment response. The dynamics of miRNAs during HBV infection are multifaceted, influenced by host variability and miRNA interactions. Given the ability of miRNAs to target multiple messenger RNA (mRNA), understanding the viral–host (human) interplay is complex but essential to develop novel clinical applications. Therefore, bioinformatics can help to analyze, identify, and interpret a vast amount of miRNA data. This review explores the bioinformatics tools available for viral and host miRNA research. Moreover, we introduce a brief overview focusing on the role of miRNAs during HBV infection. In this way, this review aims to help the selection of the most appropriate bioinformatics tools based on requirements and research goals.

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Computational Methods and Software Tools for Functional Analysis of miRNA Data

Cited by 12 publications

References 84 publications

Circulating microRNAs Suggest Networks Associated with Biological Functions in Aggressive Refractory Type 2 Celiac Disease

Circulating microRNAs Suggest Networks Associated with Biological Functions in Aggressive Refractory Type 2 Celiac Disease

Bias in miRNA enrichment analysis related to gene functional annotations

Hepatitis B Virus and microRNAs: A Bioinformatics Approach

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