Overlap of DE genes between BT642Year1 and Year1 (Splitsplines)
Seraphina Shi
This document has last been compiled on 2021-12-14 21:34:55.
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 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 BT642Year1:
Analysis of numbers of overlapping significant genes
Preflowering
Leaf
##
## Mapping BTx623 gene name to remapped gene name for BT642 :
## Out of 21505 genes with BT623 names,
## 20123 genes are matched to Remap gene names.
## Since 1652 out of 21804 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 BT642Year1 :
## ----------
## For all genes:
## BT642Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 8442 1124 465 469
## Expressed NotSig 762 8905 724 913
## NotExp Exist 59 102 0 x
## NotExist NoCorrespd 576 1213 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 7785 1005 277 0
## Expressed NotSig 560 8421 506 0
## NotExp Exist 53 91 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 657 119 188 469
## Expressed NotSig 202 484 218 913
## NotExp Exist 6 11 0 x
## NotExist NoCorrespd 576 1213 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 576 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//global_compareRemapping/leaf_Preflowering_BT642_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 469 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//global_compareRemapping/leaf_Preflowering_BT642_623_Sig_Remap_NotExist.tsv
Root
##
## Mapping BTx623 gene name to remapped gene name for BT642 :
## Out of 23695 genes with BT623 names,
## 22191 genes are matched to Remap gene names.
## Since 1885 out of 23968 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 BT642Year1 :
## ----------
## For all genes:
## BT642Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 15498 707 506 866
## Expressed NotSig 902 4297 554 638
## NotExp Exist 99 51 0 x
## NotExist NoCorrespd 1438 603 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 14337 640 276 0
## Expressed NotSig 650 4006 418 0
## NotExp Exist 88 46 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 1161 67 230 866
## Expressed NotSig 252 291 136 638
## NotExp Exist 11 5 0 x
## NotExist NoCorrespd 1438 603 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 1438 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//global_compareRemapping/root_Preflowering_BT642_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 866 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//global_compareRemapping/root_Preflowering_BT642_623_Sig_Remap_NotExist.tsv
Postflowering
Leaf
##
## Mapping BTx623 gene name to remapped gene name for BT642 :
## Out of 21505 genes with BT623 names,
## 20123 genes are matched to Remap gene names.
## Since 1652 out of 21804 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 BT642Year1 :
## ----------
## For all genes:
## BT642Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 4911 779 239 303
## Expressed NotSig 1057 12486 950 1079
## NotExp Exist 39 122 0 x
## NotExist NoCorrespd 422 1367 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 4592 698 126 0
## Expressed NotSig 809 11672 657 0
## NotExp Exist 35 109 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 319 81 113 303
## Expressed NotSig 248 814 293 1079
## NotExp Exist 4 13 0 x
## NotExist NoCorrespd 422 1367 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 422 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//global_compareRemapping/leaf_Postflowering_BT642_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 303 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//global_compareRemapping/leaf_Postflowering_BT642_623_Sig_Remap_NotExist.tsv
Root
##
## Mapping BTx623 gene name to remapped gene name for BT642 :
## Out of 23695 genes with BT623 names,
## 22191 genes are matched to Remap gene names.
## Since 1885 out of 23968 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 BT642Year1 :
## ----------
## For all genes:
## BT642Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 8604 806 296 425
## Expressed NotSig 1091 10903 764 1079
## NotExp Exist 48 102 0 x
## NotExist NoCorrespd 615 1426 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 7956 742 151 0
## Expressed NotSig 796 10139 543 0
## NotExp Exist 42 92 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 648 64 145 425
## Expressed NotSig 295 764 221 1079
## NotExp Exist 6 10 0 x
## NotExist NoCorrespd 615 1426 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 615 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//global_compareRemapping/root_Postflowering_BT642_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 425 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//global_compareRemapping/root_Postflowering_BT642_623_Sig_Remap_NotExist.tsv
Log fold changes of overlapping significant genes
Genes expressend in both Year1 and BT642Year1
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 BT642Year1 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 BT642Year1
Histograms
Session Info
## [1] "2021-12-14 21:36:29 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