This document has last been compiled on 2021-12-14 21:36:32.

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 Year1) and on data when it was mapped to specific genotype, BTx642 or RTx430, (we will call it BT642Year1). In this report, we will analyze the overlap of DE genes identified between Year1 and BT642Year1, 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 Year1 and BT642Year1:

Preflowering

Analysis of numbers of overlapping significant genes

Leaf

## 
##  
## Whether (significantly) expressed in both Year1 and BT642Year1 :
## ----------
## For all genes:
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 13416       1493      9777     1422      
##        Expressed NotSig      3941        250412    313199   38656     
##        NotExp    Exist       104         2150      0        x         
##        NotExist  NoCorrespd  1260        23786     x        x         
## 
## ----------
## For genes with 1-1 Correspondence
##    (BT642-BT623 is 1-1):
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 12664       1322      8733     0         
##        Expressed NotSig      2837        231971    280539   0         
##        NotExp    Exist       87          1929      0        x         
##        NotExist  NoCorrespd  0           0         x        x         
## 
## ----------
## For genes without 1-1 Correspondence
##    (BT642-BT623 is not 1-1):
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 752         171       1044     1422      
##        Expressed NotSig      1104        18441     32660    38656     
##        NotExp    Exist       17          221       0        x         
##        NotExist  NoCorrespd  1260        23786     x        x

Plots for numbers of overlapping significant genes

## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
##  We found 1260 genes from leaf and Preflowering that are significant in the BT642Year1 but not exist (no correspondence) in Year1, they are saved in:
## results/BT642Year1/interestingGeneSets//tps_compareRemapping/leaf_Preflowering_BT642_Remap_Sig_623_NotExist.tsv 
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
##  We found 1422 genes from leaf and Preflowering that are significant in the Year1 but not exist (no correspondence) in BT642Year1, they are saved in:
## results/Year1/interestingGeneSets//tps_compareRemapping/leaf_Preflowering_BT642_623_Sig_Remap_NotExist.tsv

Root

## 
##  
## Whether (significantly) expressed in both Year1 and BT642Year1 :
## ----------
## For all genes:
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 13416       1493      9777     1422      
##        Expressed NotSig      3941        250412    313199   38656     
##        NotExp    Exist       104         2150      0        x         
##        NotExist  NoCorrespd  1260        23786     x        x         
## 
## ----------
## For genes with 1-1 Correspondence
##    (BT642-BT623 is 1-1):
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 12664       1322      8733     0         
##        Expressed NotSig      2837        231971    280539   0         
##        NotExp    Exist       87          1929      0        x         
##        NotExist  NoCorrespd  0           0         x        x         
## 
## ----------
## For genes without 1-1 Correspondence
##    (BT642-BT623 is not 1-1):
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 752         171       1044     1422      
##        Expressed NotSig      1104        18441     32660    38656     
##        NotExp    Exist       17          221       0        x         
##        NotExist  NoCorrespd  1260        23786     x        x

Plots for numbers of overlapping significant genes

## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
##  We found 847 genes from root and Preflowering that are significant in the BT642Year1 but not exist (no correspondence) in Year1, they are saved in:
## results/BT642Year1/interestingGeneSets//tps_compareRemapping/root_Preflowering_BT642_Remap_Sig_623_NotExist.tsv 
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
##  We found 1367 genes from root and Preflowering that are significant in the Year1 but not exist (no correspondence) in BT642Year1, they are saved in:
## results/Year1/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 BT642Year1 and log-FC of Year1.
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 Year1 or BT642Year1, 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 Year1 and BT642Year1 :
## ----------
## For all genes:
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 13416       1493      9777     1422      
##        Expressed NotSig      3941        250412    313199   38656     
##        NotExp    Exist       104         2150      0        x         
##        NotExist  NoCorrespd  1260        23786     x        x         
## 
## ----------
## For genes with 1-1 Correspondence
##    (BT642-BT623 is 1-1):
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 12664       1322      8733     0         
##        Expressed NotSig      2837        231971    280539   0         
##        NotExp    Exist       87          1929      0        x         
##        NotExist  NoCorrespd  0           0         x        x         
## 
## ----------
## For genes without 1-1 Correspondence
##    (BT642-BT623 is not 1-1):
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 752         171       1044     1422      
##        Expressed NotSig      1104        18441     32660    38656     
##        NotExp    Exist       17          221       0        x         
##        NotExist  NoCorrespd  1260        23786     x        x

Plots for numbers of overlapping significant genes
Genotype: BT642

Genotype: RT430

Genotype: GenoDiff

## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
##  We found 1260 genes from leaf and Postflowering that are significant in the BT642Year1 but not exist (no correspondence) in Year1, they are saved in:
## results/BT642Year1/interestingGeneSets//tps_compareRemapping/leaf_Postflowering_BT642_Remap_Sig_623_NotExist.tsv 
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
##  We found 1422 genes from leaf and Postflowering that are significant in the Year1 but not exist (no correspondence) in BT642Year1, they are saved in:
## results/Year1/interestingGeneSets//tps_compareRemapping/leaf_Postflowering_BT642_623_Sig_Remap_NotExist.tsv

Root

For all genotypes:

## 
##  
## Whether (significantly) expressed in both Year1 and BT642Year1 :
## ----------
## For all genes:
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 13416       1493      9777     1422      
##        Expressed NotSig      3941        250412    313199   38656     
##        NotExp    Exist       104         2150      0        x         
##        NotExist  NoCorrespd  1260        23786     x        x         
## 
## ----------
## For genes with 1-1 Correspondence
##    (BT642-BT623 is 1-1):
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 12664       1322      8733     0         
##        Expressed NotSig      2837        231971    280539   0         
##        NotExp    Exist       87          1929      0        x         
##        NotExist  NoCorrespd  0           0         x        x         
## 
## ----------
## For genes without 1-1 Correspondence
##    (BT642-BT623 is not 1-1):
##                              BT642Year1                               
##                              Expressed   Expressed NotExp   NotExist  
##                              Significant NotSig    Exist    NoCorrespd
## Year1  Expressed Significant 752         171       1044     1422      
##        Expressed NotSig      1104        18441     32660    38656     
##        NotExp    Exist       17          221       0        x         
##        NotExist  NoCorrespd  1260        23786     x        x

Plots for numbers of overlapping significant genes
Genotype: BT642

Genotype: RT430

Genotype: GenoDiff

## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
##  We found 847 genes from root and Postflowering that are significant in the BT642Year1 but not exist (no correspondence) in Year1, they are saved in:
## results/BT642Year1/interestingGeneSets//tps_compareRemapping/root_Postflowering_BT642_Remap_Sig_623_NotExist.tsv 
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
##  We found 1367 genes from root and Postflowering that are significant in the Year1 but not exist (no correspondence) in BT642Year1, they are saved in:
## results/Year1/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 BT642Year1 and log-FC of Year1.
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 Year1 or BT642Year1, 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 21:49:27 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