Identification of common key genes and pathways between Covid-19 and lung cancer by using protein-protein interaction network analysis

  1. Kang Soon Nan
  2. Kalimuthu Karuppanan
  3. Suresh Kumar

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Abstract

COVID-19 is indeed an infection that is caused by a recently found coronavirus group, a type of virus proven to cause human respiratory diseases. The high mortality rate was observed in patients who had pre-existing health conditions like cancer. However, the molecular mechanism of SARS-CoV-2 infection in lung cancer patients was not discovered yet at the pathway level. This study was about determining the common key genes of COVID-19 and lung cancer through network analysis. The hub genes associated with COVID-19 and lung cancer were identified through Protein-Protein interaction analysis. The hub genes are ALB, CXCL8, FGF2, IL6, INS, MMP2, MMP9, PTGS2, STAT3 and VEGFA. Through gene enrichment, it is identified both COVID-19 and lung cancer have a common pathway in EGFR tyrosine kinase inhibitor resistance, IL-17 signalling pathway, AGE-RAGE signalling pathway in diabetic complications, HIF-1 signalling pathway and pathways in cancer.

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  1. ScreenIT

    SciScore for 10.1101/2021.02.16.431364: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The common overlapping genes of COVID-19 and lung cancer genes were obtained from venny tools (https://bioinfogp.cnb.csic.es/tools/venny/).
    https://bioinfogp.cnb.csic.es/tools/venny/
    suggested: (Venny 2.1, RRID:SCR_016561)
    PPI interaction analysis: In this research, Cytoscape (https://cytoscape.org) is being used to construct and display the network of the protein-to-protein interaction of the intermediate genes between COVID-19 and lung cancer.
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)
    https://cytoscape.org
    suggested: (CluePedia Cytoscape plugin, RRID:SCR_015784)
    STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) (https://string-db.org/) in molecular biology is a biological database as well as the web platform of documented and anticipated protein-protein interactions.
    STRING
    suggested: (STRING, RRID:SCR_005223)
    Determination of Hub Genes: All potential hub genes of a particular disease are discovered through the usage of cytoHubba, an application that is installed and executed in Cytoscape.
    cytoHubba
    suggested: (cytoHubba, RRID:SCR_017677)
    Functional Enrichment of Hub Genes: For the hub genes enrichment further studies purposes, we have been using WebGestalt (WEB-based GEne SeT Analysis Toolkit) to do so.
    WebGestalt
    suggested: None

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.02.16.431364 on bioRxiv