Overlap of DE genes between BT642Year2 and Year2 (Splitsplines)
Seraphina Shi
This document has last been compiled on 2021-12-14 23:14:59.
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 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 Year2 and BT642Year2:
Analysis of numbers of overlapping significant genes
Preflowering
Leaf
##
## Mapping BTx623 gene name to remapped gene name for BT642 :
## Out of 22408 genes with BT623 names,
## 20949 genes are matched to Remap gene names.
## Since 1729 out of 22705 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 Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 6464 1288 254 384
## Expressed NotSig 652 11694 894 1075
## NotExp Exist 34 92 0 x
## NotExist NoCorrespd 471 1486 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 5991 1172 108 0
## Expressed NotSig 438 10974 620 0
## NotExp Exist 24 84 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 473 116 146 384
## Expressed NotSig 214 720 274 1075
## NotExp Exist 10 8 0 x
## NotExist NoCorrespd 471 1486 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 471 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//global_compareRemapping/leaf_Preflowering_BT642_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 384 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//global_compareRemapping/leaf_Preflowering_BT642_623_Sig_Remap_NotExist.tsv
Root
##
## Mapping BTx623 gene name to remapped gene name for BT642 :
## Out of 24086 genes with BT623 names,
## 22572 genes are matched to Remap gene names.
## Since 1922 out of 24370 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 Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 13889 740 531 747
## Expressed NotSig 802 6277 617 767
## NotExp Exist 64 45 0 x
## NotExist NoCorrespd 1127 972 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 12792 669 286 0
## Expressed NotSig 554 5920 459 0
## NotExp Exist 59 38 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 1097 71 245 747
## Expressed NotSig 248 357 158 767
## NotExp Exist 5 7 0 x
## NotExist NoCorrespd 1127 972 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 1127 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//global_compareRemapping/root_Preflowering_BT642_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 747 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//global_compareRemapping/root_Preflowering_BT642_623_Sig_Remap_NotExist.tsv
Postflowering
Leaf
##
## Mapping BTx623 gene name to remapped gene name for BT642 :
## Out of 22408 genes with BT623 names,
## 20949 genes are matched to Remap gene names.
## Since 1729 out of 22705 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 Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 749 710 61 74
## Expressed NotSig 105 18534 1087 1385
## NotExp Exist 6 120 0 x
## NotExist NoCorrespd 50 1907 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 681 662 16 0
## Expressed NotSig 50 17182 712 0
## NotExp Exist 4 104 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 68 48 45 74
## Expressed NotSig 55 1352 375 1385
## NotExp Exist 2 16 0 x
## NotExist NoCorrespd 50 1907 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 50 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//global_compareRemapping/leaf_Postflowering_BT642_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 74 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//global_compareRemapping/leaf_Postflowering_BT642_623_Sig_Remap_NotExist.tsv
Root
##
## Mapping BTx623 gene name to remapped gene name for BT642 :
## Out of 24086 genes with BT623 names,
## 22572 genes are matched to Remap gene names.
## Since 1922 out of 24370 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 Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 7358 676 237 363
## Expressed NotSig 1214 12460 911 1151
## NotExp Exist 40 69 0 x
## NotExist NoCorrespd 538 1561 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 6838 607 112 0
## Expressed NotSig 888 11602 633 0
## NotExp Exist 35 62 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 520 69 125 363
## Expressed NotSig 326 858 278 1151
## NotExp Exist 5 7 0 x
## NotExist NoCorrespd 538 1561 x x
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 538 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//global_compareRemapping/root_Postflowering_BT642_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 363 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//global_compareRemapping/root_Postflowering_BT642_623_Sig_Remap_NotExist.tsv
Log fold changes of overlapping significant genes
Genes expressend in both Year2 and BT642Year2
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 BT642Year2 and log-FC of Year2.
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 Year2 or BT642Year2
Histograms
Session Info
## [1] "2021-12-14 23:16:21 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