Overlap of DE genes between BT642Year2 and Year2 (Combined)
Seraphina Shi
This document has last been compiled on 2021-12-14 23:30:34.
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 jump analysis.
Here we consider our combined significance pvalue, based on combining significance from:
* the splines DE
* the jump DE (at first sampled point after water is turned on)
* the splines genotype DE
We will bring in and intersect the results from the combined significance (DE_combined.csv).
Below is the analysis of overlap from DE_combine genes between Year2 and BT642Year2:
Tables for numbers of overlapping significant genes
Preflowering & Leaf
## 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 5317 2010 470 459
## Expressed NotSig 766 12005 678 1000
## NotExp Exist 26 100 0 x
## NotExist NoCorrespd 409 1548 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 4921 1866 279 0
## Expressed NotSig 572 11216 449 0
## NotExp Exist 18 90 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 396 144 191 459
## Expressed NotSig 194 789 229 1000
## NotExp Exist 8 10 0 x
## NotExist NoCorrespd 409 1548 x x## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 409 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//combined_compareRemapping/leaf_Preflowering_Remap_Sig_623_NotExist.tsv
##
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 459 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//combined_compareRemapping/leaf_Preflowering_623_Sig_Remap_NotExist.tsvPreflowering & Root
## 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 13455 2852 871 1023
## Expressed NotSig 519 4882 277 491
## NotExp Exist 60 49 0 x
## NotExist NoCorrespd 1031 1068 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 12320 2649 547 0
## Expressed NotSig 385 4581 198 0
## NotExp Exist 55 42 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 1135 203 324 1023
## Expressed NotSig 134 301 79 491
## NotExp Exist 5 7 0 x
## NotExist NoCorrespd 1031 1068 x x## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 1031 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//combined_compareRemapping/root_Preflowering_Remap_Sig_623_NotExist.tsv
##
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 1023 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//combined_compareRemapping/root_Preflowering_623_Sig_Remap_NotExist.tsvPostflowering & Leaf
## 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 421 1556 175 136
## Expressed NotSig 47 18074 973 1323
## NotExp Exist 4 122 0 x
## NotExist NoCorrespd 23 1934 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 370 1463 93 0
## Expressed NotSig 25 16717 635 0
## NotExp Exist 3 105 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 51 93 82 136
## Expressed NotSig 22 1357 338 1323
## NotExp Exist 1 17 0 x
## NotExist NoCorrespd 23 1934 x x## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 23 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//combined_compareRemapping/leaf_Postflowering_Remap_Sig_623_NotExist.tsv
##
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 136 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//combined_compareRemapping/leaf_Postflowering_623_Sig_Remap_NotExist.tsvPostflowering & Root
## 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 6342 1852 321 377
## Expressed NotSig 1053 12461 827 1137
## NotExp Exist 29 80 0 x
## NotExist NoCorrespd 436 1663 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 5876 1715 170 0
## Expressed NotSig 792 11552 575 0
## NotExp Exist 24 73 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 466 137 151 377
## Expressed NotSig 261 909 252 1137
## NotExp Exist 5 7 0 x
## NotExist NoCorrespd 436 1663 x x## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 436 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//combined_compareRemapping/root_Postflowering_Remap_Sig_623_NotExist.tsv
##
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 377 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//combined_compareRemapping/root_Postflowering_623_Sig_Remap_NotExist.tsvPlots for numbers of overlapping significant genes
Session Info
## [1] "2021-12-14 23:31:37 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