Overlap of DE genes between BT642Year1 and Year1 (JUMP)
Seraphina Shi
This document has last been compiled on 2021-12-14 21:50:34.
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 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.
We will bring in and intersect the file DE_jumps which gives the significant genes when comparing the first time point after the watering change to that before; significant genes will be those where the difference between before and after is not the same in control and treatment. Water change for pre-flowering drought refers to when water is resumed; water change for post-flowering drought refers to the first time point after the control is irrigated and the treatment is not (thus for treatment samples it does NOT refer to the time since watering, but the length of time since the treatment plants’ water exposure has been different than control).
Below is the analysis of overlap from DE_jump genes between Year1 and BT642Year1:
For the water change week, we collected data at day 56 and 63 for Preflowering and day 63 and 70 for Postflowering in Year 1. We will analysis the overlapping genes of the week jump, Day63-Day56 for Preflowering and Day70-Day63 for Postflowering
Week Jump
Preflowering, Day63 - Day56
Below is the analysis of the weekly timepoint (Week 8/Day 56 vs Week 9/Day 63) from DE_jumps genes between Year1 and BT642Year1.
Analysis of numbers of overlapping significant genes
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.Day063 vs Day056 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year1 and BT642Year1 :
## ----------
## For all genes:
## BT642Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 2496 257 374 105
## Expressed NotSig 353 15179 2279 1277
## NotExp Exist 130 979 0 x
## NotExist NoCorrespd 180 1609 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 2314 227 182 0
## Expressed NotSig 274 14084 1473 0
## NotExp Exist 117 899 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 182 30 192 105
## Expressed NotSig 79 1095 806 1277
## NotExp Exist 13 80 0 x
## NotExist NoCorrespd 180 1609 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 180 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day063_vs_Day056_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 105 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day063_vs_Day056_623_Sig_Remap_NotExist.tsv
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.Day063 vs Day056 : root BT642
##
##
##
## Whether (significantly) expressed in both Year1 and BT642Year1 :
## ----------
## For all genes:
## BT642Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 5260 603 1694 300
## Expressed NotSig 337 13286 1952 1204
## NotExp Exist 1125 943 0 x
## NotExist NoCorrespd 438 1603 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 4851 549 1184 0
## Expressed NotSig 253 12168 1322 0
## NotExp Exist 1057 889 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 409 54 510 300
## Expressed NotSig 84 1118 630 1204
## NotExp Exist 68 54 0 x
## NotExist NoCorrespd 438 1603 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 438 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day063_vs_Day056_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 300 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day063_vs_Day056_623_Sig_Remap_NotExist.tsv
Log fold changes of overlapping significant genes
Scatter plots
MA plots
The MA plot visualizes the differences between 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 \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year1 or BT642Year1
Since some significantly expressed genes are only expressed in one year, (either Year1 or BT642Year1), we provide the following histograms to visualize their log fold change values.
Postflowering, Day70 - Day63
Below is the analysis of the weekly timepoint (Week 9/Day 63 vs Week 10/Day 70) from DE_jumps genes between Year1 and BT642Year1.
Analysis of numbers of overlapping significant genes
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.Day070 vs Day063 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year1 and BT642Year1 :
## ----------
## For all genes:
## BT642Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 6 18 3 0
## Expressed NotSig 0 18862 1739 1382
## NotExp Exist 1 507 0 x
## NotExist NoCorrespd 0 1789 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 6 14 1 0
## Expressed NotSig 0 17434 1099 0
## NotExp Exist 1 460 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 0 4 2 0
## Expressed NotSig 0 1428 640 1382
## NotExp Exist 0 47 0 x
## NotExist NoCorrespd 0 1789 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 0 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//de_jumps_compareRemapping/leaf_Postflowering_BT642_Day070_vs_Day063_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 0 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//de_jumps_compareRemapping/leaf_Postflowering_BT642_Day070_vs_Day063_623_Sig_Remap_NotExist.tsv
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.Day070 vs Day063 : root BT642
##
##
##
## Whether (significantly) expressed in both Year1 and BT642Year1 :
## ----------
## For all genes:
## BT642Year1
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year1 Expressed Significant 486 291 72 32
## Expressed NotSig 61 19449 2654 1472
## NotExp Exist 17 1250 0 x
## NotExist NoCorrespd 29 2012 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 450 272 24 0
## Expressed NotSig 40 17834 1707 0
## NotExp Exist 16 1155 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 36 19 48 32
## Expressed NotSig 21 1615 947 1472
## NotExp Exist 1 95 0 x
## NotExist NoCorrespd 29 2012 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 29 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//de_jumps_compareRemapping/root_Postflowering_BT642_Day070_vs_Day063_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 32 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//de_jumps_compareRemapping/root_Postflowering_BT642_Day070_vs_Day063_623_Sig_Remap_NotExist.tsv
Log fold changes of overlapping significant genes
Scatter plots
MA plots
The MA plot visualizes the differences between 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 \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year1 or BT642Year1
Since some significantly expressed genes are only expressed in one year, (either Year1 or BT642Year1), we provide the following histograms to visualize their log fold change values.
