Selected article for: "cell type and enrichment analysis"
Author: Satria P. Sajuthi; Peter DeFord; Nathan D. Jackson; Michael T. Montgomery; Jamie L. Everman; Cydney L. Rios; Elmar Pruesse; James D. Nolin; Elizabeth G. Plender; Michael E. Wechsler; Angel CY Mak; Celeste Eng; Sandra Salazar; Vivian Medina; Eric M. Wohlford; Scott Huntsman; Deborah A. Nickerson; Soren Germer; Michael C. Zody; Gonçalo Abecasis; Hyun Min Kang; Kenneth M. Rice; Rajesh Kumar; Sam Oh; Jose Rodriguez-Santana; Esteban G. Burchard; Max A. Seibold
Title: Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium
  • Document date: 2020_4_10
    • ID: mj8ebo7i_30
    Snippet: Genes were required to have an FDR adjusted p-value < 0.05, and an absolute log 2 FC 745 > 0.5 to be considered significant. Based on these cutoffs, genes were classified as 746 being shared if they were significant in both comparisons, or as CoV + -specfic or HRV + -747 specific if significant in only one comparison. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.09.034454 doi: bioRx.....
    Document: Genes were required to have an FDR adjusted p-value < 0.05, and an absolute log 2 FC 745 > 0.5 to be considered significant. Based on these cutoffs, genes were classified as 746 being shared if they were significant in both comparisons, or as CoV + -specfic or HRV + -747 specific if significant in only one comparison. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.09.034454 doi: bioRxiv preprint the rest in order to obtain gene log 2 FC values for each cell type with which to rank order 766 the genes. Gene set enrichment analysis (GSEA) was then used to test for association 767 between upregulated genes in the shared, CoV + -specific, and HRV + -specific gene sets 768 and each of the cell types, based on the cell type-specific ordered gene lists. GSEA was 769 carried out using the FGSEA R package (v1.12.0). The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.09.034454 doi: bioRxiv preprint

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