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HGNC Genes

SARS-CoV-2 proteins

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SARS-CoV-2 Proteins
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    Transcriptome Profiling of different types of human respiratory tract cells infected by SARS-CoV-2 Highlight an unique Role for Inflammatory and Interferon Response

    Authors: Luping Lei; Qiumei Cao; Yu Wang; Mario Hensen; Anu V. Chandran; Michelle L. Hill; J.L. Kiappes; Raymond A. Dwek; Dominic S. Alonzi; Weston B. Struwe; Nicole Zitzmann; Florian M Wurm; Xin Zheng; Jia Liu; Davey Smith; Daniela Weiskopf; Alessandro Sette; Shane Crotty; Jian Jin; Xian Chen; Andrew Pekosz; Sabra Klein; Irina Burd

    doi:10.1101/2020.11.15.383927 Date: 2020-11-16 Source: bioRxiv

    The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease MESHD ( COVID-19 MESHD) at the end of 2019 has caused a large global outbreak and now become a major public health issue. Lack of data underlying how the human host interacts with SARS-CoV-2 virus. In the current study, We performed Venn-analysis, Gene ontology (GO), KEGG pathway analysis and Protein-protein interaction analysis of whole transcriptome studies with the aim of clarifying the genes and pathways potentially altered during human respiratory tract cells infected with SARS-CoV-2. We selected four studies through a systematic search of the Gene Expression Omnibus (GEO) database or published article about SARS-CoV-2 infection MESHD in different types of respiratory tract cells. We found 36 overlapping upregulated genes among different types of cells after viral infection. Further functional enrichment analysis revealed these DEGs are most likely involved in biological processes related to inflammatory response and response to cytokine, cell component related to extracellular space and I-kappaB/NF-kappaB complex, molecular function related to protein binding and cytokine activity. KEGG pathways analysis highlighted altered conical and casual pathways related to TNF HGNC, NF-kappa B HGNC, Cytokine-cytokine receptor interaction and IL17 HGNC signaling pathways during SARS-CoV-2 infection MESHD with CXCL1 HGNC, CXCL2 HGNC, CXCL3 HGNC, CXCL8 HGNC, CXCL10 HGNC, IL32 HGNC, CX3CL1 HGNC, CCL20 HGNC, IRF1 HGNC, NFKB2 HGNC and NFKB1A up-regulated which may explain the inflammatory cytokine storms associated with severe cases of COVID-19 MESHD.

    Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

    Authors: Mariana Ferrarini; Avantika Lal; Rita Rebollo; Andreas Gruber; Andrea Guarracino; Itziar Martinez Gonzalez; Taylor Floyd; Daniel Siqueira de Oliveira; Justin Shanklin; Ethan Beausoleil; Taneli Pusa; Brett Pickett; Vanessa Aguiar-Pulido

    doi:10.21203/rs.3.rs-63136/v1 Date: 2020-08-20 Source: ResearchSquare

    The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic ( COVID-19 MESHD) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected MESHD cells. Well-known immunoregulators including CSF2 HGNC, IL-32 HGNC, IL-6 HGNC and SERPINA3 HGNC were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1 HGNC, PABPC1 HGNC and eIF4b HGNC, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19 MESHD. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2.

    Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

    Authors: Mariana G. Ferrarini; Avantika Lal; Rita Rebollo; Andreas Gruber; Andrea Guarracino; Itziar Martinez Gonzalez; Taylor Floyd; Daniel Siqueira de Oliveira; Justin Shanklin; Ethan Beausoleil; Taneli Pusa; Brett Pickett; Vanessa Aguiar-Pulido

    doi:10.1101/2020.07.28.225581 Date: 2020-07-29 Source: bioRxiv

    The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic ( COVID-19 MESHD) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected MESHD cells. Well-known immunoregulators including CSF2 HGNC, IL-32 HGNC, IL-6 HGNC and SERPINA3 HGNC were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1 HGNC, PABPC1 HGNC and eIF4b HGNC, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19 MESHD. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).
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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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