Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and tre
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ORIGINAL ARTICLE
Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID‑19) diagnosis and treatment using microarray dataset and bioinformatics methods Basavaraj Vastrad1 · Chanabasayya Vastrad2 · Anandkumar Tengli3 Received: 21 May 2020 / Accepted: 20 August 2020 © King Abdulaziz City for Science and Technology 2020
Abstract The goal of the present investigation is to identify the differentially expressed genes (DEGs) between SARS-CoV-2 infected and normal control samples to investigate the molecular mechanisms of infection with SARS-CoV-2. The microarray data of the dataset E-MTAB-8871 were retrieved from the ArrayExpress database. Pathway and Gene Ontology (GO) enrichment study, protein–protein interaction (PPI) network, modules, target gene–miRNA regulatory network, and target gene–TF regulatory network have been performed. Subsequently, the key genes were validated using an analysis of the receiver operating characteristic (ROC) curve. In SARS-CoV-2 infection, a total of 324 DEGs (76 up- and 248 down-regulated genes) were identified and enriched in a number of associated SARS-CoV-2 infection pathways and GO terms. Hub and target genes such as TP53, HRAS, MAPK11, RELA, IKZF3, IFNAR2, SKI, TNFRSF13C, JAK1, TRAF6, KLRF2, CD1A were identified from PPI network, target gene–miRNA regulatory network, and target gene–TF regulatory network. Study of the ROC showed that ten genes (CCL5, IFNAR2, JAK2, MX1, STAT1, BID, CD55, CD80, HAL-B, and HLA-DMA) were substantially involved in SARS-CoV-2 patients. The present investigation identified key genes and pathways that deepen our understanding of the molecular mechanisms of SARS-CoV-2 infection, and could be used for SARS-CoV-2 infection as diagnostic and therapeutic biomarkers. Keywords SARS-CoV-2 infection · Bioinformatics analysis · Biomarkers · Protein–protein interaction (PPI) network · Differentially expressed genes
Introduction Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) infection is known as novel coronavirus disease-2019 (COVID-19) and has spread widely throughout the globe in an epidemic proportion with the current pandemic risk (Li et al. 2020). This infection is related to respiratory diseases, and this virus mainly infects respiratory * Chanabasayya Vastrad [email protected] 1
Department of Pharmaceutics, SET`S College of Pharmacy, Dharwad, Karnataka 580002, India
2
Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka 580001, India
3
Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru and JSS Academy of Higher Education & Research, Mysuru, Karnataka 570015, India
epithelial cells and transmits from human to human primarily through the respiratory tract, contributing to more deaths (Zou et al. 2020; Madurai Elavarasan and Pugazhendhi 2020). In the present situation, the survival rate of patients with SARS-CoV-2 infection has been slightly increased, and patients with this infection have no apparent benefit from the curre
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