ArticleComputers in biology and medicine2021
Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection.
Article in Computers in biology and medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it, 45 citations in OpenAlex.
- Pooled it
- MicroRNA-driven evolutionary pressure in SARS-CoV-2: the role of hsa-miR-6512 in mutational dynamics.Scientific reports · 2025Article
- Characterization of SARS-CoV-2 Entry Genes in Skeletal Muscle and Impacts of In Vitro Versus In Vivo Infection.Journal of cachexia, sarcopenia and muscle · 2025Article
- Comprehensive computational analysis of differentially expressed miRNAs and their influence on transcriptomic signatures in prostate cancer.Scientific reports · 2025Article
- Dysregulated Urinary Extracellular Vesicle Small RNAs in Diabetic Nephropathy: Implications for Diagnosis and Therapy.Journal of the Endocrine Society · 2024Article
- A Machine Learning Approach to Identify Potential miRNA-Gene Regulatory Network Contributing to the Pathogenesis of SARS-CoV-2 Infection.Biochemical genetics · 2024Article
- Whole transcriptome landscape in HAPE under the stress of environment at high altitudes: new insights into the mechanisms of hypobaric hypoxia tolerance.Frontiers in immunology · 2024Article
- Therapeutic effects of platelet-derived extracellular vesicles on viral myocarditis correlate with biomolecular content.Frontiers in immunology · 2024Article
- Circulating hsa-miR-320a and its regulatory network in type 1 diabetes mellitus.Frontiers in immunology · 2024Article
- Macrophage Activation Syndrome in Coinciding Pandemics of Obesity and COVID-19: Worse than Bad.Advances in experimental medicine and biology · 2024Review
- Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression.Frontiers in immunology · 2024Article
- Analyzing the role of ACE2, AR, MX1 and TMPRSS2 genetic markers for COVID-19 severity.Human genomics · 2023Article
- Shared miRNA landscapes of COVID-19 and neurodegeneration confirm neuroinflammation as an important overlapping feature.Frontiers in molecular neuroscience · 2023Article
- Circulating microRNAs as emerging regulators of COVID-19.Theranostics · 2023Review
- Identification of 3 key genes as novel diagnostic and therapeutic targets for OA and COVID-19.Frontiers in immunology · 2023Article
- Identifying MicroRNA Markers That Predict COVID-19 Severity Using Machine Learning Methods.Life (Basel, Switzerland) · 2022Article
- miRNA expression in COVID-19.Gene reports · 2022Review
- Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype.iScience · 2022Article
- Gene Network Analysis of the Transcriptome Impact of SARS-CoV-2 Interacting MicroRNAs in COVID-19 Disease.International journal of molecular sciences · 2022Review
- Identifying significant genes and functionally enriched pathways in familial hypercholesterolemia using integrated gene co-expression network analysis.Saudi journal of biological sciences · 2022Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe spread of a novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) has affected both the public health and the global economy. The current study was aimed at analysing the genetic sequence of this highly contagious corona virus from an evolutionary perspective, comparing the genetic variation features of different geographic strains, and identifying the key miRNAs as well as their gene targets from the transcriptome data of infected lung tissues.
methodsA multilevel robust computational analysis was undertaken for viral genetic sequence alignment, phylogram construction, genome-wide transcriptome data interpretation of virus-infected lung tissues, miRNA mapping, and functional biology networking.
resultsOur findings show both genetic similarities as well as notable differences in the S protein length among SARS-CoV-1, SARS-CoV-2 and MERS viruses. All SARS-CoV-2 strains showed a high genetic similarity with the parent Wuhan strain, but Saudi Arabian, South African, USA, Russia and New Zealand strains carry 3 additional genetic variations like P333L (RNA -dependant RNA polymerase), D614G (spike), and P4715L (ORF1ab). The infected lung tissues demonstrated the upregulation of 282 (56.51%) antiviral defensive response pathway genes and downregulation of 217 (43.48%) genes involved in autophagy and lung repair pathways. By miRNA mapping, 4 key miRNAs (hsa-miR-342-5p, hsa-miR-432-5p, hsa-miR-98-5p and hsa-miR-17-5p), targeting multiple host genes (MYC, IL6, ICAM1 and VEGFA) as well as SARS-CoV2 gene (ORF1ab) were identified.
conclusionSystems biology methods offer a new perspective in understanding the molecular basis for the faster spread of SARS-CoV-2 infection. The antiviral miRNAs identified in this study may aid in the ongoing search for novel personalized therapeutic avenues for COVID patients.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.