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Differential expression results: dendritic cells vs monocytes

Source: R/de_celltype_results.R
de_celltype_results.Rd

DESeq2 results comparing in vitro differentiated dendritic cells (moDC or tolDC) against monocytes, within each group (healthy controls and SLE patients). Used in the lesson about monocyte differentiation (l5_DEGs_monocytes_diff_es; Figures 4 and 5 of the article).

Usage

de_celltype_results

Format

A named list with four data frames (Ctrl_moDC, Ctrl_tolDC, SLE_moDC, SLE_tolDC), each with 21,718 rows (genes) and 7 columns: gene, baseMean, log2FoldChange, lfcSE, stat, pvalue and padj (see de_results).

Source

Generated from filtered_txi and metadata_cleaned.

Details

Designs (all genes of filtered_txi, reference level monocyte):

  • Controls: ~ Cell_type.

  • SLE patients: ~ SLEDAI_category + Cell_type + Dose_category (adjusted for disease activity and glucocorticoid dose).

Results were extracted with results(alpha = 0.05, name = "Cell_type_<moDC|tolDC>_vs_monocyte") (Wald test, Benjamini-Hochberg adjustment).

With |log2FoldChange| >= 1 and padj < 0.05 (up / down): Ctrl moDC 2688 / 2947, Ctrl tolDC 2731 / 2849, SLE moDC 2945 / 3652 and SLE tolDC 2804 / 3596. The article (DESeq2 on R 4.0.2) reports the same numbers for moDC and differs by a few genes in tolDC (2736 / 2851 and 2804 / 3592). The script that generates this object is data-raw/lesson5_checkpoints.R.

See also

de_results (SLE vs Ctrl within each cell type).

Examples

names(de_celltype_results)
#> [1] "Ctrl_moDC"  "Ctrl_tolDC" "SLE_moDC"   "SLE_tolDC" 
head(de_celltype_results$Ctrl_moDC[order(de_celltype_results$Ctrl_moDC$padj), ])
#>         gene  baseMean log2FoldChange     lfcSE     stat        pvalue
#> 11881   MRC1 68435.137       9.146538 0.2613979 34.99086 3.098523e-268
#> 17371 SLC7A8  4486.754       8.216655 0.2413625 34.04280 5.187183e-254
#> 6460   GPNMB 64903.360       9.443920 0.2816243 33.53376 1.553122e-246
#> 19706  TREM2  6019.286      10.614697 0.3247763 32.68310 2.714885e-234
#> 4641    ECM1  2623.108       7.358515 0.2325977 31.63623 1.172972e-219
#> 890     APOE 70848.544      11.967432 0.3869356 30.92874 4.907850e-210
#>                padj
#> 11881 4.765219e-264
#> 17371 3.988684e-250
#> 6460  7.961823e-243
#> 19706 1.043806e-230
#> 4641  3.607826e-216
#> 890   1.257964e-206