Identification of COVID-19 subtypes based on immunogenomic profiling

  1. Zuobing Chen
  2. Qiushi Feng
  3. Tianfang Zhang
  4. Xiaosheng Wang

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Abstract

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  1. Version published to 10.1016/j.intimp.2021.107615
  2. ScreenIT

    SciScore for 10.1101/2021.01.24.21250387: (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
    Datasets: We downloaded the RNA-Seq gene expression profile datasets in leukocyte samples from 100 COVID-19 patients (GSE157103) and in SARS-CoV-2-infected human tissues from nasopharyngeal swabs (GSE152075 and GSE156063) from the Gene Expression Omnibus (GEO) (
    Gene Expression Omnibus
    suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
    Based on the differentially expressed genes, we identified KEGG (26) pathways differentially enriched between ICU and non-ICU COVID-19 patients by (27) with a threshold of FDR < 0.05.
    KEGG
    suggested: (KEGG, RRID:SCR_012773)

    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

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  3. Version published to 10.1101/2021.01.24.21250387 on medRxiv