Overlap of DE genes between RT430Year1 and Year1 (Splitsplines)
Seraphina Shi
This document has last been compiled on 2021-12-14 21:35:27.
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 RT430Year1). In this report, we will analyze the overlap of DE genes identified between Year1 and RT430Year1, focusing on the results from DE spline analysis.
We will bring in and intersect the results from the splines significance (DE_splitsplines.csv). These are genes that are found different between treatment and control after fitting a spline function to the gene data separately for treatment and control, and asking whether there is any significant difference between the two functions.
Below is the analysis of overlap from DE_splitsplines genes between Year1 and RT430Year1:
Analysis of numbers of overlapping significant genes
Preflowering
Leaf
##
## Mapping BTx623 gene name to remapped gene name for RT430 :
## Out of 21505 genes with BT623 names,
## 20203 genes are matched to Remap gene names.
## Since 1668 out of 21846 remap gene names are mapped to multiple BT623 gene names,
## we collapsed on BT623 with average values so that each remap gene name has a unique row.
##
## Whether (significantly) expressed in both Year1 and RT430Year1 :
## ----------
## For all genes:
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 5510 906 305 284
## Expressed NotSig 930 11536 1357 1018
## NotExp Exist 32 108 0 x
## NotExist NoCorrespd 310 1242 x x
##
## ----------
## For genes with 1-1 Correspondence
## (RT430-BT623 is 1-1):
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 5167 833 169 0
## Expressed NotSig 689 10768 994 0
## NotExp Exist 28 92 0 x
## NotExist NoCorrespd 0 0 x x
##
## ----------
## For genes without 1-1 Correspondence
## (RT430-BT623 is not 1-1):
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 343 73 136 284
## Expressed NotSig 241 768 363 1018
## NotExp Exist 4 16 0 x
## NotExist NoCorrespd 310 1242 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 310 genes from leaf and Preflowering that are significant in the RT430Year1 but not exist (no correspondence) in Year1, they are saved in:
## results/RT430Year1/interestingGeneSets//global_compareRemapping/leaf_Preflowering_RT430_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 284 genes from leaf and Preflowering that are significant in the Year1 but not exist (no correspondence) in RT430Year1, they are saved in:
## results/Year1/interestingGeneSets//global_compareRemapping/leaf_Preflowering_RT430_623_Sig_Remap_NotExist.tsv
Root
##
## Mapping BTx623 gene name to remapped gene name for RT430 :
## Out of 23695 genes with BT623 names,
## 22267 genes are matched to Remap gene names.
## Since 1888 out of 23994 remap gene names are mapped to multiple BT623 gene names,
## we collapsed on BT623 with average values so that each remap gene name has a unique row.
##
## Whether (significantly) expressed in both Year1 and RT430Year1 :
## ----------
## For all genes:
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 16040 903 677 922
## Expressed NotSig 639 3539 768 506
## NotExp Exist 94 41 0 x
## NotExist NoCorrespd 1319 448 x x
##
## ----------
## For genes with 1-1 Correspondence
## (RT430-BT623 is 1-1):
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 14902 792 436 0
## Expressed NotSig 423 3270 577 0
## NotExp Exist 90 36 0 x
## NotExist NoCorrespd 0 0 x x
##
## ----------
## For genes without 1-1 Correspondence
## (RT430-BT623 is not 1-1):
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 1138 111 241 922
## Expressed NotSig 216 269 191 506
## NotExp Exist 4 5 0 x
## NotExist NoCorrespd 1319 448 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 1319 genes from root and Preflowering that are significant in the RT430Year1 but not exist (no correspondence) in Year1, they are saved in:
## results/RT430Year1/interestingGeneSets//global_compareRemapping/root_Preflowering_RT430_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 922 genes from root and Preflowering that are significant in the Year1 but not exist (no correspondence) in RT430Year1, they are saved in:
## results/Year1/interestingGeneSets//global_compareRemapping/root_Preflowering_RT430_623_Sig_Remap_NotExist.tsv
Postflowering
Leaf
##
## Mapping BTx623 gene name to remapped gene name for RT430 :
## Out of 21505 genes with BT623 names,
## 20203 genes are matched to Remap gene names.
## Since 1668 out of 21846 remap gene names are mapped to multiple BT623 gene names,
## we collapsed on BT623 with average values so that each remap gene name has a unique row.
##
## Whether (significantly) expressed in both Year1 and RT430Year1 :
## ----------
## For all genes:
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 6996 1186 491 393
## Expressed NotSig 547 10153 1171 909
## NotExp Exist 58 82 0 x
## NotExist NoCorrespd 422 1130 x x
##
## ----------
## For genes with 1-1 Correspondence
## (RT430-BT623 is 1-1):
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 6554 1089 331 0
## Expressed NotSig 323 9491 832 0
## NotExp Exist 49 71 0 x
## NotExist NoCorrespd 0 0 x x
##
## ----------
## For genes without 1-1 Correspondence
## (RT430-BT623 is not 1-1):
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 442 97 160 393
## Expressed NotSig 224 662 339 909
## NotExp Exist 9 11 0 x
## NotExist NoCorrespd 422 1130 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 422 genes from leaf and Postflowering that are significant in the RT430Year1 but not exist (no correspondence) in Year1, they are saved in:
## results/RT430Year1/interestingGeneSets//global_compareRemapping/leaf_Postflowering_RT430_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 393 genes from leaf and Postflowering that are significant in the Year1 but not exist (no correspondence) in RT430Year1, they are saved in:
## results/Year1/interestingGeneSets//global_compareRemapping/leaf_Postflowering_RT430_623_Sig_Remap_NotExist.tsv
Root
##
## Mapping BTx623 gene name to remapped gene name for RT430 :
## Out of 23695 genes with BT623 names,
## 22267 genes are matched to Remap gene names.
## Since 1888 out of 23994 remap gene names are mapped to multiple BT623 gene names,
## we collapsed on BT623 with average values so that each remap gene name has a unique row.
##
## Whether (significantly) expressed in both Year1 and RT430Year1 :
## ----------
## For all genes:
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 10838 1132 563 554
## Expressed NotSig 813 8338 882 874
## NotExp Exist 55 80 0 x
## NotExist NoCorrespd 637 1130 x x
##
## ----------
## For genes with 1-1 Correspondence
## (RT430-BT623 is 1-1):
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 10034 1038 346 0
## Expressed NotSig 569 7746 667 0
## NotExp Exist 49 77 0 x
## NotExist NoCorrespd 0 0 x x
##
## ----------
## For genes without 1-1 Correspondence
## (RT430-BT623 is not 1-1):
## RT430Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 804 94 217 554
## Expressed NotSig 244 592 215 874
## NotExp Exist 6 3 0 x
## NotExist NoCorrespd 637 1130 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 637 genes from root and Postflowering that are significant in the RT430Year1 but not exist (no correspondence) in Year1, they are saved in:
## results/RT430Year1/interestingGeneSets//global_compareRemapping/root_Postflowering_RT430_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 554 genes from root and Postflowering that are significant in the Year1 but not exist (no correspondence) in RT430Year1, they are saved in:
## results/Year1/interestingGeneSets//global_compareRemapping/root_Postflowering_RT430_623_Sig_Remap_NotExist.tsv
Log fold changes of overlapping significant genes
Genes expressend in both Year1 and RT430Year1
Scatter plot
Because of the equation for calculating the log-FC for DE_spline, \(lfc = sign(\frac{1}{T} \sum_{t=1}^T lfc(t)) \times (\frac{1}{T} \sum_{t=1}^T |lfc(t)|)\), the signs of log fold changes might be off. For the scatter plots, we will plot the absolute value of Log fold changes.
MA plot
The MA plot visualizes the differences between absolute values of log-FC of RT430Year1 and log-FC of Year1.
The y-axis is \(M = |\text{lfc}_{\text{Remap}}| - |\text{lfc}_{\text{623}}|\) and the x-axis is \(A = \frac{|\text{lfc}_{\text{Remap}}| + |\text{lfc}_{\text{623}}|}{2}\) 
Significant genes only expressend in Year1 or RT430Year1
Histograms
Session Info
## [1] "2021-12-14 21:36:52 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