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    • Differential Expression

    We utilized MAST to perform comparisons between treated and untreated single cell samples for each subject and cell type in the HIRISA collection. To ensure robust comparisons, we utilized a sampling and bootstrapping approach for each comparison, then summarized the results of comparisons across subjects. For additional details, see the Data Analysis Methods section.

    Results are provided below for comparisons at two cell type resolutions that align to the Human Immune Health Atlas:

    AIFI_L1: Broad cell type classes
    AIFI_L2: Mid-resolution cell type classes

    Descriptions of the columns in these results are available by clicking the header below.

    DEG Results columns
    AIFI_L1 or AIFI_L2: Cell type used for differential expression tests
    cell_type_label: Cell type label used in figures and visualization tools
    fg: Foreground condition in the contrast (IFN used for stimulation)
    bg: Background condition in the contrast ("none", i.e. untreated, for all comparisons in HIRISA)
    gene: Gene symbol for the contrast test
    median_log2fc: Median of Log2(Fold Change) results across subjects.
    min_log2fc: Minimum of Log2(Fold Change) results across subjects (more stringent)
    median_adjp: Median of multiple hypothesis test-adjusted P-values across subjects.
    max_adjp: Maximum of multiple hypothesis test-adjusted P-values across subjects (more stringent).
    mean: Mean of normalized gene expression for all cells of the cell type, fg, and bg condition used for analysis. 

    HIRISA Differential Expression results
    File Name Description Download Link
    hirisa_deg_AIFI_L1_2026-05-19.csv DEG results for broad populations (L1)
    hirisa_deg_AIFI_L2_2026-05-19.csv DEG results for mid-resolution populations (L2)