Differential gene expression results for all celltypes and timepoints

# check
dim(marker_genes.df)
## [1] 9368    9
head(marker_genes.df)
## # A tibble: 6 x 9
## # Groups:   timepoint, celltype [4]
##   gene       p_val avg_log2FC pct.1 pct.2 p_val_adj timepoint celltype DE_status
##   <chr>      <dbl>      <dbl> <dbl> <dbl>     <dbl> <fct>     <fct>    <fct>    
## 1 CHCHD2 0              0.828 0.631 0.387 0         2         ExDp2    Signific~
## 2 PGRMC1 0              0.541 0.875 0.853 0         2         ExDp2    Signific~
## 3 CHCHD2 0              0.650 0.415 0.156 0         4         ExDp1    Signific~
## 4 CHCHD2 0              0.836 0.415 0.167 0         4         ExDp2    Signific~
## 5 RP11-~ 0             -0.702 0.562 0.705 0         4         ExDp2    Signific~
## 6 CHCHD2 1.60e-277      0.635 0.584 0.396 6.72e-273 6         Ast      Signific~
summary(marker_genes.df)
##      gene               p_val             avg_log2FC          pct.1       
##  Length:9368        Min.   :0.000e+00   Min.   :-2.4943   Min.   :0.0160  
##  Class :character   1st Qu.:0.000e+00   1st Qu.:-0.4559   1st Qu.:0.3540  
##  Mode  :character   Median :1.368e-06   Median :-0.3378   Median :0.5140  
##                     Mean   :9.608e-04   Mean   :-0.3024   Mean   :0.5461  
##                     3rd Qu.:5.084e-04   3rd Qu.:-0.2717   3rd Qu.:0.7280  
##                     Max.   :9.998e-03   Max.   : 2.1378   Max.   :1.0000  
##                                                                           
##      pct.2          p_val_adj       timepoint    celltype   
##  Min.   :0.0200   Min.   :0.00000   2:2211    ExDp2  :2020  
##  1st Qu.:0.4890   1st Qu.:0.00000   4:1513    ExM-U  :1640  
##  Median :0.6540   Median :0.05737   6:5644    ExM    :1020  
##  Mean   :0.6467   Mean   :0.43926             ExDp1  : 934  
##  3rd Qu.:0.8180   3rd Qu.:1.00000             vRG    : 669  
##  Max.   :1.0000   Max.   :1.00000             PgS    : 503  
##                                               (Other):2582  
##                             DE_status   
##  Significantly expressed in V337M:9368  
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Results distributions

P-values

## Warning: Removed 2357 rows containing non-finite values (stat_bin).
## Warning: Removed 2 rows containing missing values (geom_bar).

## Warning: Removed 507 rows containing non-finite values (stat_bin).
## Warning: Removed 28 rows containing missing values (geom_bar).

## Warning: Removed 143 rows containing non-finite values (stat_bin).
## Removed 28 rows containing missing values (geom_bar).

## Warning: Removed 1707 rows containing non-finite values (stat_bin).
## Removed 28 rows containing missing values (geom_bar).

Average log fold changes of gene expression in FTD-mutants relative to normal

Note on interpretation

In this context, positive log fold change values indicate that the gene is more highly expressed in mutant cells relative to normal, and vice versa for negative values.

Top 10 genes differentially expressed at each timepoint for each celltype

Volcano Plots of differential expression for each celltype and timepoint

Astrocytes

Ventricular Radial Glia

Outer Radial Glia

Excittaory Deep Layer Neurons 1

Excitatory Deep Layer Neurons 2

Excitatory Neurons (Newborn)

Exitatory Neurons (Maturing)

Excitatory Neurons (Maturing, Upper-enriched)

Interneurons MGE

Interneurons CGE

Oligodendrocyte Precursors

Intermediate Progenitors

Progenitors, S phase

Progenitors, G2M phase

Investigating XIST expression across celltypes

Results summary:

Summary of XIST differential expression in neuronal celltypes
Timepoint Celltypes differentially expressing XIST Avg. log 2 fold change in expression in FTD-mutant cells from controls
2 months ExDp1, InCGE, InMGE, ExM, vRG, ExM-U, oRG, PgS -0.763
4 months ExDp2, ExDp1, ExN, ExM, PgG2M, oRG, IP, vRG, PgS, Ast, InMGE 0.611
6 months ExDp2, ExN, ExM, Ast, ExM-U, ExDp1, IP, vRG, oRG, PgG2M, OPC, PgS 0.829

Detailed statistics by timepoint:

Instances of XIST differential expression in V337M cells, 2 months
Gene D.E. status Developmental timepoint (month) Cell Type P value Avg. log2 fold change Percent V337M cells of this celltype expressing
XIST Significantly expressed in V337M 2 ExDp1 0.0e+00 -1.2977e+00 1.44e-01
XIST Significantly expressed in V337M 2 InCGE 0.0e+00 -4.4540e-01 2.10e-01
XIST Significantly expressed in V337M 2 InMGE 0.0e+00 -4.5190e-01 1.94e-01
XIST Significantly expressed in V337M 2 ExM 0.0e+00 -1.2966e+00 9.00e-02
XIST Significantly expressed in V337M 2 vRG 0.0e+00 -5.7820e-01 1.40e-01
XIST Significantly expressed in V337M 2 ExM-U 0.0e+00 -3.6120e-01 1.08e-01
XIST Significantly expressed in V337M 2 oRG 1.9e-03 -8.6210e-01 1.37e-01
XIST Significantly expressed in V337M 2 PgS 4.8e-03 -8.0950e-01 1.61e-01
Instances of XIST differential expression in V337M cells, 4 months
Gene D.E. status Developmental timepoint (month) Cell Type P value Avg. log2 fold change Percent V337M cells of this celltype expressing
XIST Significantly expressed in V337M 4 ExDp2 0e+00 8.845e-01 2.93e-01
XIST Significantly expressed in V337M 4 ExDp1 0e+00 8.577e-01 3.57e-01
XIST Significantly expressed in V337M 4 ExN 0e+00 9.342e-01 3.33e-01
XIST Significantly expressed in V337M 4 ExM 0e+00 7.508e-01 2.80e-01
XIST Significantly expressed in V337M 4 PgG2M 0e+00 7.126e-01 3.55e-01
XIST Significantly expressed in V337M 4 oRG 0e+00 8.213e-01 3.68e-01
XIST Significantly expressed in V337M 4 IP 0e+00 6.029e-01 3.16e-01
XIST Significantly expressed in V337M 4 vRG 0e+00 5.630e-01 3.44e-01
XIST Significantly expressed in V337M 4 PgS 0e+00 6.303e-01 3.24e-01
XIST Significantly expressed in V337M 4 Ast 0e+00 2.733e-01 2.68e-01
XIST Significantly expressed in V337M 4 InMGE 1e-04 -3.124e-01 1.18e-01
Instances of XIST differential expression in V337M cells, 6 months
Gene D.E. status Developmental timepoint (month) Cell Type P value Avg. log2 fold change Percent V337M cells of this celltype expressing
XIST Significantly expressed in V337M 6 ExDp2 0e+00 8.3760e-01 3.36e-01
XIST Significantly expressed in V337M 6 ExN 0e+00 1.7327e+00 4.29e-01
XIST Significantly expressed in V337M 6 ExM 0e+00 1.6416e+00 3.74e-01
XIST Significantly expressed in V337M 6 Ast 0e+00 5.0840e-01 4.35e-01
XIST Significantly expressed in V337M 6 ExM-U 0e+00 4.9110e-01 2.57e-01
XIST Significantly expressed in V337M 6 ExDp1 0e+00 6.0170e-01 2.65e-01
XIST Significantly expressed in V337M 6 IP 0e+00 1.3553e+00 4.19e-01
XIST Significantly expressed in V337M 6 vRG 0e+00 7.8150e-01 3.57e-01
XIST Significantly expressed in V337M 6 oRG 0e+00 7.1380e-01 3.72e-01
XIST Significantly expressed in V337M 6 PgG2M 0e+00 3.6670e-01 3.62e-01
XIST Significantly expressed in V337M 6 OPC 0e+00 5.2120e-01 4.20e-01
XIST Significantly expressed in V337M 6 PgS 0e+00 3.9670e-01 3.44e-01