This document has last been compiled on 2021-12-14 23:16:24.

We ran the same analysis pipeline from preprocessing to differential gene expression (DE) analysis on data when it was mapped to BTx623 (we will call it Year2) and on data when it was mapped to specific genotype, BTx642 or RTx430, (we will call it BT642Year2). In this report, we will analyze the overlap of DE genes identified between Year2 and BT642Year2, focusing on the results from DE spline analysis.

We will bring in and intersect the results from the timepoint significance. These are genes that are found different between treatment and control in a specific timepoint.

Below is the analysis of overlap from DE_splitsplines genes between Year2 and BT642Year2:

Preflowering

Analysis of numbers of overlapping significant genes

Leaf

## 
##  
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 5861        868       5710     802       
##        Expressed NotSig      2510        312329    352594   45886     
##        NotExp    Exist       31          1985      0        x         
##        NotExist  NoCorrespd  562         30750     x        x         
## 
## ----------
## For genes with 1-1 Correspondence
##    (BT642-BT623 is 1-1):
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 5543        775       5232     0         
##        Expressed NotSig      1888        288994    315264   0         
##        NotExp    Exist       23          1705      0        x         
##        NotExist  NoCorrespd  0           0         x        x         
## 
## ----------
## For genes without 1-1 Correspondence
##    (BT642-BT623 is not 1-1):
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 318         93        478      802       
##        Expressed NotSig      622         23335     37330    45886     
##        NotExp    Exist       8           280       0        x         
##        NotExist  NoCorrespd  562         30750     x        x

Plots for numbers of overlapping significant genes

## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
##  We found 562 genes from leaf and Preflowering that are significant in the BT642Year2 but not exist (no correspondence) in Year2, they are saved in:
## results/BT642Year2/interestingGeneSets//tps_compareRemapping/leaf_Preflowering_BT642_Remap_Sig_623_NotExist.tsv 
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
##  We found 802 genes from leaf and Preflowering that are significant in the Year2 but not exist (no correspondence) in BT642Year2, they are saved in:
## results/Year2/interestingGeneSets//tps_compareRemapping/leaf_Preflowering_BT642_623_Sig_Remap_NotExist.tsv

Root

## 
##  
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 5861        868       5710     802       
##        Expressed NotSig      2510        312329    352594   45886     
##        NotExp    Exist       31          1985      0        x         
##        NotExist  NoCorrespd  562         30750     x        x         
## 
## ----------
## For genes with 1-1 Correspondence
##    (BT642-BT623 is 1-1):
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 5543        775       5232     0         
##        Expressed NotSig      1888        288994    315264   0         
##        NotExp    Exist       23          1705      0        x         
##        NotExist  NoCorrespd  0           0         x        x         
## 
## ----------
## For genes without 1-1 Correspondence
##    (BT642-BT623 is not 1-1):
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 318         93        478      802       
##        Expressed NotSig      622         23335     37330    45886     
##        NotExp    Exist       8           280       0        x         
##        NotExist  NoCorrespd  562         30750     x        x

Plots for numbers of overlapping significant genes

## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
##  We found 274 genes from root and Preflowering that are significant in the BT642Year2 but not exist (no correspondence) in Year2, they are saved in:
## results/BT642Year2/interestingGeneSets//tps_compareRemapping/root_Preflowering_BT642_Remap_Sig_623_NotExist.tsv 
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
##  We found 411 genes from root and Preflowering that are significant in the Year2 but not exist (no correspondence) in BT642Year2, they are saved in:
## results/Year2/interestingGeneSets//tps_compareRemapping/root_Preflowering_BT642_623_Sig_Remap_NotExist.tsv

Log fold changes of overlapping significant genes

Scatter plot

MA plot

The MA plot visualizes the differences between log-FC of BT642Year2 and log-FC of Year2.
The y-axis is \(M = \text{lfc}_{\text{RemapYear}} - \text{lfc}_{\text{Year}}\) and the x-axis is \(A = \frac{\text{lfc}_{\text{RemapYear}} + \text{lfc}_{\text{Year}}}{2}\)

Histograms

Histograms of the log-fold change for genes that are significant in one of Year2 or BT642Year2, but not even expressed in the other (and thus are filtered out and have no ability to have a p-value or lfc value assigned to them).

Postflowering

Analysis of numbers of overlapping significant genes

Leaf

For all genotypes:

## 
##  
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 5861        868       5710     802       
##        Expressed NotSig      2510        312329    352594   45886     
##        NotExp    Exist       31          1985      0        x         
##        NotExist  NoCorrespd  562         30750     x        x         
## 
## ----------
## For genes with 1-1 Correspondence
##    (BT642-BT623 is 1-1):
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 5543        775       5232     0         
##        Expressed NotSig      1888        288994    315264   0         
##        NotExp    Exist       23          1705      0        x         
##        NotExist  NoCorrespd  0           0         x        x         
## 
## ----------
## For genes without 1-1 Correspondence
##    (BT642-BT623 is not 1-1):
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 318         93        478      802       
##        Expressed NotSig      622         23335     37330    45886     
##        NotExp    Exist       8           280       0        x         
##        NotExist  NoCorrespd  562         30750     x        x

Plots for numbers of overlapping significant genes
Genotype: BT642

Genotype: RT430

Genotype: GenoDiff

## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
##  We found 562 genes from leaf and Postflowering that are significant in the BT642Year2 but not exist (no correspondence) in Year2, they are saved in:
## results/BT642Year2/interestingGeneSets//tps_compareRemapping/leaf_Postflowering_BT642_Remap_Sig_623_NotExist.tsv 
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
##  We found 802 genes from leaf and Postflowering that are significant in the Year2 but not exist (no correspondence) in BT642Year2, they are saved in:
## results/Year2/interestingGeneSets//tps_compareRemapping/leaf_Postflowering_BT642_623_Sig_Remap_NotExist.tsv

Root

For all genotypes:

## 
##  
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 5861        868       5710     802       
##        Expressed NotSig      2510        312329    352594   45886     
##        NotExp    Exist       31          1985      0        x         
##        NotExist  NoCorrespd  562         30750     x        x         
## 
## ----------
## For genes with 1-1 Correspondence
##    (BT642-BT623 is 1-1):
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 5543        775       5232     0         
##        Expressed NotSig      1888        288994    315264   0         
##        NotExp    Exist       23          1705      0        x         
##        NotExist  NoCorrespd  0           0         x        x         
## 
## ----------
## For genes without 1-1 Correspondence
##    (BT642-BT623 is not 1-1):
##                              BT642Year2                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year2  Expressed Significant 318         93        478      802       
##        Expressed NotSig      622         23335     37330    45886     
##        NotExp    Exist       8           280       0        x         
##        NotExist  NoCorrespd  562         30750     x        x

Plots for numbers of overlapping significant genes
Genotype: BT642

Genotype: RT430

Genotype: GenoDiff

## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
##  We found 274 genes from root and Postflowering that are significant in the BT642Year2 but not exist (no correspondence) in Year2, they are saved in:
## results/BT642Year2/interestingGeneSets//tps_compareRemapping/root_Postflowering_BT642_Remap_Sig_623_NotExist.tsv 
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
##  We found 411 genes from root and Postflowering that are significant in the Year2 but not exist (no correspondence) in BT642Year2, they are saved in:
## results/Year2/interestingGeneSets//tps_compareRemapping/root_Postflowering_BT642_623_Sig_Remap_NotExist.tsv

Log fold changes of overlapping significant genes

Scatter plot

MA plot

The MA plot visualizes the differences between log-FC of BT642Year2 and log-FC of Year2.
The y-axis is \(M = \text{lfc}_{\text{RemapYear}} - \text{lfc}_{\text{Year}}\) and the x-axis is \(A = \frac{\text{lfc}_{\text{RemapYear}} + \text{lfc}_{\text{Year}}}{2}\)

Histograms

Histograms of the log-fold change for genes that are significant in one of Year2 or BT642Year2, but not even expressed in the other (and thus are filtered out and have no ability to have a p-value or lfc value assigned to them).

Session Info

## [1] "2021-12-14 23:30:27 PST"
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] cowplot_1.1.1  readr_2.0.2    tidyr_1.1.4    purrr_0.3.4    stringr_1.4.0 
##  [6] gridExtra_2.3  ggplot2_3.3.5  dplyr_1.0.7    rmarkdown_2.11 knitr_1.36    
## [11] SCF_4.1.0     
## 
## loaded via a namespace (and not attached):
##  [1] highr_0.9        pillar_1.6.4     bslib_0.3.1      compiler_4.1.2  
##  [5] jquerylib_0.1.4  tools_4.1.2      bit_4.0.4        digest_0.6.28   
##  [9] lubridate_1.8.0  jsonlite_1.7.2   evaluate_0.14    lifecycle_1.0.1 
## [13] tibble_3.1.6     gtable_0.3.0     pkgconfig_2.0.3  rlang_0.4.12    
## [17] DBI_1.1.1        parallel_4.1.2   yaml_2.2.1       xfun_0.28       
## [21] fastmap_1.1.0    withr_2.4.2      hms_1.1.1        generics_0.1.1  
## [25] vctrs_0.3.8      sass_0.4.0       bit64_4.0.5      tidyselect_1.1.1
## [29] glue_1.5.0       R6_2.5.1         fansi_0.5.0      vroom_1.5.5     
## [33] farver_2.1.0     tzdb_0.2.0       magrittr_2.0.1   scales_1.1.1    
## [37] ellipsis_0.3.2   htmltools_0.5.2  assertthat_0.2.1 colorspace_2.0-2
## [41] labeling_0.4.2   utf8_1.2.2       stringi_1.7.5    munsell_0.5.0   
## [45] crayon_1.4.2