Review of databases for experimentally validated human microRNA–mRNA interactions

Kariuki, Dorian; Asam, Kesava; Aouizerat, Bradley E.; Lewis, Kimberly; Florez, José C.; Flowers, Elena

doi:10.1093/database/baad014

Cited by 17 publications

(3 citation statements)

References 39 publications

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“…Additionally, we employed the "multiMiR" package with experimental verification to screen for miRNAs that target pyroptosisassociated hub genes from miRTarBase database [25,26]. Subsequently, we estimated the target lncRNAs of the aforementioned miRNAs from the StarBase Website (http://starbase.sysu.edu.cn/) via a clipExpNum > 7-based prediction, using experimentally validated associations as a filtering criteria [25,27]. Lastly, we visualized the generated cecRNA axis in Cytoscape software.…”

Section: Generation Of Immune Infiltration and Cerna Regulatory Axesmentioning

confidence: 99%

Identification of Pyroptosis-Related Genes Regulating the Progression of Chronic Rhinosinusitis with Nasal Polyps

Li,

Zhang,

Wang

et al. 2024

Int Arch Allergy Immunol

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Introduction: Chronic rhinosinusitis with nasal polyps (CRSwNP) is an immunologic disease, and pyroptosis, an inflammation-based cellular death, strictly modulates CRSwNP pathology, whereas the pyroptosis genes and mechanisms involved in CRSwNP remain unclear. Herein, we explored disease biomarkers and potential therapeutic targets for pyroptosis and immune regulation in CRSwNP using bioinformatics analysis and tissue-based verification. Methods: We retrieved the transcriptional profiles of the high-throughput dataset GSE136825 from the Gene Expression Omnibus database, as well as 170 pyroptosis-related gene expressions from GeneCards. Using R, we identified differentially expressed pyroptosis-related genes and examined the potential biological functions of the aforementioned genes using Gene Ontology, Kyoto Encyclopedia of the Genome pathway, immune infiltration, and protein-protein interaction (PPI) network analyses, thereby generating a list of hub genes. The hub genes were, in turn, verified using real-time quantitative polymerase chain reaction (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB). Ultimately, using the StarBase and miRTarBase databases, we estimated the targeting microRNAs and long chain non-coding RNAs. Results: We demonstrated that the identified pyroptosis-related genes primarily modulated bacterial defense activities, as well as inflammasome immune response and assembly. Moreover, they were intricately linked to neutrophil and macrophage infiltration. Furthermore, we validated the tissue contents of hub genes AIM2, NLPR6, and CASP5 and examined potential associations with clinical variables. We also developed a competitive endogenous RNA (ceRNA) modulatory axis to examine possible underlying molecular mechanisms. Conclusion: We found AIM2, CASP5, and NLRP6, three hub genes for pyroptosis in chronic rhinosinusitis with nasal polyps, by biological analysis, experimental validation, and clinical variable validation.

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Section: Generation Of Immune Infiltration and Cerna Regulatory Axesmentioning

confidence: 99%

Identification of Pyroptosis-Related Genes Regulating the Progression of Chronic Rhinosinusitis with Nasal Polyps

Li,

Zhang,

Wang

et al. 2024

Int Arch Allergy Immunol

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“…ENCORI is the second most cited database for such predictions, and miRWalk harbors experimental data from luciferase assays, microarrays, NGS, pSILAC, and western blot experiments. Furthermore, where miRWalk made up for ENCORI's last update of 2021 by being updated twice a year and containing predictions from MirTarBase, ENCORI was crucial in understanding the lncRNA interactions which miRWalk lacked [60]. miRNAs binding on 3′UTR region, having an interaction score > 0.95 , and binding gap = 1 were considered as significant and retrieved from miRWalk.…”

Section: Schizophrenia-associated 3-node Cerna Network Construction A...mentioning

confidence: 99%

Deciphering the landscape of lncRNA-driven ceRNA network in schizophrenia etiology

Mukhopadhyay,

Singh,

Dohare

et al. 2024

Egypt J Med Hum Genet

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Background The unifying hypothesis of competing endogenous RNA (ceRNA) wherein crosstalk between coding (mRNAs) and long non-coding RNAs (lncRNAs) via microRNA (miRNA) response elements, creates a pervasive regulatory network across the transcriptome, has been implicated in complex disorders including schizophrenia. Even with a wide range of high-throughput data, the etiology of schizophrenia remains elusive, necessitating a more holistic understanding of the altered genetic landscape, shifting focus from solely candidate gene studies and protein-coding variants. Objective We developed lncRNA-associated ceRNA networks to elucidate global molecular/regulatory signatures underlying schizophrenia using diverse data in the public domain. Methods Microarray dataset associated with peripheral blood mononuclear cells (PBMCs) of schizophrenia and control patients was used to identify differentially expressed mRNAs. Weighted gene co-expression network analysis (WGCNA) was used to identify highly correlated hubs, and genes from these overlapping Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) term genesets were considered key mRNA players. StarBase, Human MicroRNA Disease Database, and miRWalk were used to derive mRNA-miRNA and miRNA-lncRNA relationships. Finally, the key mRNAs, interacting lncRNAs and miRNAs were chosen to reconstruct sub-ceRNA networks based on network centrality scores. Results Bioinformatics analysis revealed the involvement of three differentially expressed mRNAs, namely ADRA1A, HAP1 and HOMER3 in the schizophrenia ceRNA networks with lncRNAs NEAT1, XIST, and KCNQ1OT1 modulating their activity by a suggestive sequestering of miR-3163, miR-214-3p and miR-2467-3p, respectively. Conclusions Furthermore, based on contextual evidence, we propose how ceRNAs could orchestrate crosstalk between neurostructural dynamics and immune/inflammatory processes and enable unifying these disparate models of schizophrenia etiology.

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“…Advanced single-cell sequencing techniques allow researchers to access highly resolved spatial transcriptomes at intercellular resolution without external perturbation [52][53][54] . Databases focusing on regulatory RNAs, such as lncRNAdb, Rfam, miRBase, starBase/ENCORI, and NONCODE, have been improved to support annotation and network analysis [55][56][57][58][59] .…”

Section: Introductionmentioning

confidence: 99%

Molecular insights into regulatory RNAs in the cellular machinery

Yang,

Kim,

Yang

et al. 2024

Exp Mol Med

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It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.

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Review of databases for experimentally validated human microRNA–mRNA interactions

Cited by 17 publications

References 39 publications

Identification of Pyroptosis-Related Genes Regulating the Progression of Chronic Rhinosinusitis with Nasal Polyps

Identification of Pyroptosis-Related Genes Regulating the Progression of Chronic Rhinosinusitis with Nasal Polyps

Deciphering the landscape of lncRNA-driven ceRNA network in schizophrenia etiology

Molecular insights into regulatory RNAs in the cellular machinery

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