ArticleGene reports2020
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19.
Article in Gene reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 47 citations in OpenAlex.
- Integrated miR-omics and proteomics reveal the regulatory role of miR in protein networks associated with COVID-19 disease progression.Frontiers in immunology · 2026Article
- Organelle-centered ISG15 biology: distinguishing covalent ISGylation from interferon-associated responses.Frontiers in immunology · 2026Review
- Genome-Wide Association Study of COVID-19 Breakthrough Infections and Genetic Overlap with Other Diseases: A Study of the UK Biobank.International journal of molecular sciences · 2025Article
- Transcriptomic analysis of differential expression between surviving and nonsurviving patients infected by the SARS-CoV-2 Delta variant.Scientific reports · 2025Article
- Transcriptomic profiling of severe and critical COVID-19 patients reveals alterations in expression, splicing and polyadenylation.Scientific reports · 2025Article
- Deep Plasma Proteomics with Data-Independent Acquisition: Clinical Study Protocol Optimization with a COVID-19 Cohort.Journal of proteome research · 2024Article
- Exploring cross-tissue DNA methylation patterns: blood-brain CpGs as potential neurodegenerative disease biomarkers.Communications biology · 2024Article
- Frequency, kinetics and determinants of viable SARS-CoV-2 in bioaerosols from ambulatory COVID-19 patients infected with the Beta, Delta or Omicron variants.Nature communications · 2024Article
- Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology.BMC bioinformatics · 2024Article
- 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
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- Identification of host genomic biomarkers from multiple transcriptomics datasets for diagnosis and therapies of SARS-CoV-2 infections.PloS one · 2023Article
- Transcriptomics secondary analysis of severe human infection with SARS-CoV-2 identifies gene expression changes and predicts three transcriptional biomarkers in leukocytes.Computational and structural biotechnology journal · 2023Article
- Identification of genes related to immune enhancement caused by heterologous ChAdOx1-BNT162b2 vaccines in lymphocytes at single-cell resolution with machine learning methods.Frontiers in immunology · 2023Article
- Deciphering the role of precursor miR-12136 and miR-8485 in the progression of intellectual disability (ID).IBRO neuroscience reports · 2022Article
- Integrated network-based multiple computational analyses for identification of co-expressed candidate genes associated with neurological manifestations of COVID-19.Scientific reports · 2022Article
- HIMA2: high-dimensional mediation analysis and its application in epigenome-wide DNA methylation data.BMC bioinformatics · 2022Article
- Network Pharmacology and Molecular Docking Elucidate the Underlying Pharmacological Mechanisms of the HerbViruses · 2022Article
- ISG15 and ISGylation in Human Diseases.Cells · 2022Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection is a leading cause of pneumonia and death. The aim of this investigation is to identify the key genes in SARS-CoV-2 infection and uncover their potential functions. We downloaded the expression profiling by high throughput sequencing of GSE152075 from the Gene Expression Omnibus database. Normalization of the data from primary SARS-CoV-2 infected samples and negative control samples in the database was conducted using R software. Then, joint analysis of the data was performed. Pathway and Gene ontology (GO) enrichment analyses were performed, and the protein-protein interaction (PPI) network, target gene - miRNA regulatory network, target gene - TF regulatory network of the differentially expressed genes (DEGs) were constructed using Cytoscape software. Identification of diagnostic biomarkers was conducted using receiver operating characteristic (ROC) curve analysis. 994 DEGs (496 up regulated and 498 down regulated genes) were identified. Pathway and GO enrichment analysis showed up and down regulated genes mainly enriched in the NOD-like receptor signaling pathway, Ribosome, response to external biotic stimulus and viral transcription in SARS-CoV-2 infection. Down and up regulated genes were selected to establish the PPI network, modules, target gene - miRNA regulatory network, target gene - TF regulatory network revealed that these genes were involved in adaptive immune system, fluid shear stress and atherosclerosis, influenza A and protein processing in endoplasmic reticulum. In total, ten genes (CBL, ISG15, NEDD4, PML, REL, CTNNB1, ERBB2, JUN, RPS8 and STUB1) were identified as good diagnostic biomarkers. In conclusion, the identified DEGs, hub genes and target genes contribute to the understanding of the molecular mechanisms underlying the advancement of SARS-CoV-2 infection and they may be used as diagnostic and molecular targets for the treatment of patients with SARS-CoV-2 infection in the future.
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