Last updated: 2025-05-15

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Knit directory: Lung_scMultiomics_paper/

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Differential gene expression analyses across tissue

Wilcoxon ranksum test at single-cell leveL gives more conservative results.

Summarizing DE genes by selecting p-value cutoffs

A table of cell counts by tissue and cell-type.

          
           lungs spleens
  Other     1654     104
  Treg      1336      47
  Th17      2732      68
  CD4_T     6980     886
  CD8_T    12210     421
  NK        8067     464
  Memory_B  5287   10507
  Naive_B   1174    1710

A barplot for number of DE genes detected for each cell type except for Th17 and Treg, due to low number of cells in spleen.

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Compare and contrast DE genes across immune subsets

A Venn diagram for DE genes shared across cell types other than memory B cells implies DE genes are cell-type specific.

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A full summary of shared and unique DE genes across cell types

UpSet-style plot only shows the count of elements specific to each intersection.

Lung up-regulated genes

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Check the lung up-regulated genes shared across all immune subsets

[1] "HSP90AA1 HSPA1A HSP90AB1 HSPD1 RPS26 DNAJB1 HSPA6 HSPA1B HSPH1 HSPE1 HSPB1 CACYBP HSPA8 UBC DOK2 BAG3 STIP1 ABHD3 PLIN2 ZFAND2A GNLY FKBP4 TNFRSF1B GBP2 CGAS MT2A HSPA4 NKG7 AHSA1 SERPINH1 CCL4L2 GZMB GIPC1"

Spleen up-regulated genes

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GO enrichment results

Lung-regulated genes

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Spleen-regulated genes

The DE genes down-regulated in lung detected from memory B cells are significantly enriched for asthma risk genes from KEGG pathway. The overlapped genes are HLA genes and CD40. Their function in B cells might be enhancing subsequent interaction with T cells.

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K-means clustering for log2FC

We performed K-means clustering over log2FC for all genes with at most one NA across cell types.

Heatmap for average log2FC for each cluster

Clustering for effect sizes does not show cell type specificity except for memory B cells.

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[1] "The pair-wise correlation of genes for most clusters form a distribution skewed to 1."

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Heatmap for average log2FC for each cell-type (Memory B excluded)

Clustering for effect sizes shows stronger cell-type specificity.

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R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

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```