Overlap of DE genes between BT642Year1 and Year1 (Combined)
Seraphina Shi
This document has last been compiled on 2021-12-14 21:49:35.
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 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 Year1 and BT642Year1:
Tables for numbers of overlapping significant genes
Preflowering & Leaf
## 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 8464 1747 672 586
## Expressed NotSig 1091 7931 517 796
## NotExp Exist 57 104 0 x
## NotExist NoCorrespd 605 1184 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 7795 1626 427 0
## Expressed NotSig 892 7458 356 0
## NotExp Exist 51 93 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 669 121 245 586
## Expressed NotSig 199 473 161 796
## NotExp Exist 6 11 0 x
## NotExist NoCorrespd 605 1184 x x## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 605 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//combined_compareRemapping/leaf_Preflowering_Remap_Sig_623_NotExist.tsv
##
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 586 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//combined_compareRemapping/leaf_Preflowering_623_Sig_Remap_NotExist.tsvPreflowering & Root
## 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 15756 2755 837 1158
## Expressed NotSig 450 2443 223 346
## NotExp Exist 99 51 0 x
## NotExist NoCorrespd 1409 632 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 14459 2550 526 0
## Expressed NotSig 353 2271 168 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 1297 205 311 1158
## Expressed NotSig 97 172 55 346
## NotExp Exist 11 5 0 x
## NotExist NoCorrespd 1409 632 x x## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 1409 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//combined_compareRemapping/root_Preflowering_Remap_Sig_623_NotExist.tsv
##
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 1158 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//combined_compareRemapping/root_Preflowering_623_Sig_Remap_NotExist.tsvPostflowering & Leaf
## 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 4190 3822 561 496
## Expressed NotSig 431 10790 628 886
## NotExp Exist 32 129 0 x
## NotExist NoCorrespd 340 1449 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 3840 3577 373 0
## Expressed NotSig 309 10045 410 0
## NotExp Exist 28 116 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 350 245 188 496
## Expressed NotSig 122 745 218 886
## NotExp Exist 4 13 0 x
## NotExist NoCorrespd 340 1449 x x## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 340 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//combined_compareRemapping/leaf_Postflowering_Remap_Sig_623_NotExist.tsv
##
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 496 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//combined_compareRemapping/leaf_Postflowering_623_Sig_Remap_NotExist.tsvPostflowering & Root
## 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 8319 2940 545 605
## Expressed NotSig 632 9513 515 899
## NotExp Exist 42 108 0 x
## NotExist NoCorrespd 552 1489 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 7635 2741 328 0
## Expressed NotSig 429 8828 366 0
## NotExp Exist 37 97 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 684 199 217 605
## Expressed NotSig 203 685 149 899
## NotExp Exist 5 11 0 x
## NotExist NoCorrespd 552 1489 x x## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 552 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//combined_compareRemapping/root_Postflowering_Remap_Sig_623_NotExist.tsv
##
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 605 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//combined_compareRemapping/root_Postflowering_623_Sig_Remap_NotExist.tsvPlots for numbers of overlapping significant genes
Session Info
## [1] "2021-12-14 21:50:32 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