GSE200028

GSE200028

Experimental design: Control mice (n=5), Short term MSc administered mice - day 2 collection (n = 5) and Long term MSc administered mice day 9 collection (n = 5)

Contrasts performed:

• Day 2 vs Control
• Day 9 vs Control
• Day 9 vs Day 2
• Day 9 private - down control + day 2 up day 8 & vice versa
• Day 2 private - seesaw trends across groups
• Day 2 + Day 9 vs control (MSC private excluding days)

## 
## FALSE  TRUE 
##     1   187

## [1] "Rab7a"

## 
## TRUE 
##   10

Efferocytotsis genes

Day 2 vs Control

Day 9 vs control

Day 9 vs Day 2

Day 9 private signature

Weak signals - adjusted p-value is poor

Day 2 private signature

day2_mat <- v$E
day2_mat <- day2_mat[stat_sig,]

day2_mat <- t(day2_mat)
day2_mat <- scale(day2_mat, center=T, scale = T)
day2_mat <- t(day2_mat)

annot_col <- data.frame(row.names = colnames(day2_mat), status = factor(c(rep("control", 5), rep("long_term", 5), rep("short_term", 5))))

cols <- c("navy", "red", "gold2")
names(cols) <- c("control", "long_term", "short_term")
annot_colors <- list(status = cols)

library(viridis)

pheatmap::pheatmap(day2_mat[,c(1,2,3,4,5,11,12,13,14,15,6,7,8,9,10)], cluster_cols = F, cluster_rows = T, show_rownames = T,
                   show_colnames = F, annotation_col = annot_col,
                   annotation_colors = annot_colors,
                   col = hcl.colors(100, "Purple-Green",rev=F),
                   main = "Efferocytosis Day 2 private signatures \n P.Value <= 0.05",
                   cutree_cols = 3)

MSC Private

stat_sig <- rownames(day2_v_ctrl)
day2_mat <- v$E
day2_mat <- day2_mat[stat_sig,]

day2_mat <- t(day2_mat)
day2_mat <- scale(day2_mat, center=T, scale = T)
day2_mat <- t(day2_mat)

annot_col <- data.frame(row.names = colnames(day2_mat), status = factor(c(rep("control", 5), rep("long_term", 5), rep("short_term", 5))))

cols <- c("navy", "red", "gold2")
names(cols) <- c("control", "long_term", "short_term")
annot_colors <- list(status = cols)

library(viridis)

pheatmap::pheatmap(day2_mat[,c(1,2,3,4,5,11,12,13,14,15,6,7,8,9,10)], cluster_cols = F, cluster_rows = T, show_rownames = T,
                   show_colnames = F, annotation_col = annot_col,
                   annotation_colors = annot_colors,
                   col = hcl.colors(100, "Purple-Green",rev=F),
                   main = "Efferocytosis MSC private signatures \n P.Value <= 0.05",
                   cutree_cols = 3)

Fibrosis genes

Day 2 vs Control

Day 9 vs control

Day 9 vs Day 2

Day 9 private signature

Day 2 private signature

MSC Private

stat_sig <- rownames(day2_v_ctrl)
day2_mat <- v$E
day2_mat <- day2_mat[stat_sig,]

day2_mat <- t(day2_mat)
day2_mat <- scale(day2_mat, center=T, scale = T)
day2_mat <- t(day2_mat)

annot_col <- data.frame(row.names = colnames(day2_mat), status = factor(c(rep("control", 5), rep("long_term", 5), rep("short_term", 5))))

cols <- c("navy", "red", "gold2")
names(cols) <- c("control", "long_term", "short_term")
annot_colors <- list(status = cols)

library(viridis)

pheatmap::pheatmap(day2_mat[,c(1,2,3,4,5,11,12,13,14,15,6,7,8,9,10)], cluster_cols = F, cluster_rows = T, show_rownames = T,
                   show_colnames = F, annotation_col = annot_col,
                   annotation_colors = annot_colors,
                   col = hcl.colors(100, "Purple-Green",rev=F),
                   main = "Fibrosis MSC private signatures \n P.Value <= 0.05",
                   cutree_cols = 3)