Identify lung-specific transcriptomic features
2025-12-08
Last updated: 2025-12-08
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Knit directory: Lung_scMultiomics_paper/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | b5746be | Jing Gu | 2025-12-08 | identify bulk-level DE results |
Differential gene expression analyses with DESeq2
log(Counts) ~ factor(submission_date) + Race + Age + Sex + Tissue
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 1710A barplot for number of DE genes detected for each cell type except for Th17 and Treg, due to low number of cells in spleen.
A combined volcano plot for DE genes across cell types
DE statistics for the GNLY example
baseMean log2FoldChange lfcSE stat pvalue padj gene
1 1757.30559 2.323263 0.5248658 4.426395 9.582078e-06 9.551590e-04 GNLY
2 535.68527 6.856581 1.3146697 5.215440 1.833813e-07 1.275976e-05 GNLY
3 37.37406 4.564120 0.7593359 6.010673 1.847542e-09 1.420298e-06 GNLY
cluster avg_log2FC group
1 NK 2.323263 Lung Up-regulated
2 Memory_B 6.856581 Lung Up-regulated
3 Naive_B 4.564120 Lung Up-regulatedGO enrichment for cross-tissue genes
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
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ggrepel_0.9.6 SingleCellExperiment_1.20.1
[3] cowplot_1.1.3 ComplexHeatmap_2.14.0
[5] htmltools_0.5.8.1 scales_1.4.0
[7] colorRamp2_0.1.0 tidyr_1.3.1
[9] dplyr_1.1.4 rhdf5_2.42.1
[11] SummarizedExperiment_1.28.0 Biobase_2.58.0
[13] MatrixGenerics_1.10.0 Rcpp_1.0.14
[15] Matrix_1.6-5 GenomicRanges_1.50.2
[17] GenomeInfoDb_1.34.9 IRanges_2.32.0
[19] S4Vectors_0.36.2 BiocGenerics_0.44.0
[21] matrixStats_1.5.0 data.table_1.17.4
[23] stringr_1.5.1 plyr_1.8.9
[25] magrittr_2.0.3 ggplot2_3.5.2
[27] gtable_0.3.6 gtools_3.9.5
[29] gridExtra_2.3 ArchR_1.0.2
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