Overlap of DE genes between BT642Year2 and Year2 (JUMP)
Seraphina Shi
This document has last been compiled on 2021-12-14 23:31:39.
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.
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 Year2 and BT642Year2:
For the water change week, we collected data at day 56, 58, 59, 61 and 63 for Preflowering and day 63, 65, 68 and 70 for Postflowering. We will analysis the overlapping genes of the week jump, Day63-Day56 for Preflowering and Day70-Day63 for Postflowering, between Year2 and the remapped Year2 first. Then we will analysis the overlapping genes of the days jump, Day58-Day56, Day59-Day58, Day61-Day59, Day63-Day61 for Preflowering and Day65-Day63, Day68-Day65, Day70-Day68 for Postflowering between Year2 and the remapped Year2
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 Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day063 vs Day056 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 105 28 19 7
## Expressed NotSig 58 19453 1812 1452
## NotExp Exist 8 572 0 x
## NotExist NoCorrespd 11 1946 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 97 27 7 0
## Expressed NotSig 46 17986 1140 0
## NotExp Exist 7 520 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 8 1 12 7
## Expressed NotSig 12 1467 672 1452
## NotExp Exist 1 52 0 x
## NotExist NoCorrespd 11 1946 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 11 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day063_vs_Day056_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 7 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day063_vs_Day056_623_Sig_Remap_NotExist.tsv
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.Day063 vs Day056 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 1417 141 222 51
## Expressed NotSig 194 19343 1921 1463
## NotExp Exist 70 652 0 x
## NotExist NoCorrespd 61 2038 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 1315 125 68 0
## Expressed NotSig 160 17768 1244 0
## NotExp Exist 65 599 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 102 16 154 51
## Expressed NotSig 34 1575 677 1463
## NotExp Exist 5 53 0 x
## NotExist NoCorrespd 61 2038 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 61 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day063_vs_Day056_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 51 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//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 BT642Year2 and log-FC of Year2.
The y-axis is \(M = \text{lfc}_{\text{remap}} - \text{lfc}_{\text{623}}\) and the x-axis is \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), 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 Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day070 vs Day063 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 0 0 0 0
## Expressed NotSig 0 19916 1389 1459
## NotExp Exist 0 308 0 x
## NotExist NoCorrespd 0 1957 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 0 0 0 0
## Expressed NotSig 0 18407 896 0
## NotExp Exist 0 276 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 0 0 0 0
## Expressed NotSig 0 1509 493 1459
## NotExp Exist 0 32 0 x
## NotExist NoCorrespd 0 1957 x xPlots for numbers of overlapping significant genes：
## Not significant genes to make visualizations.
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 0 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//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 Year2 but not exist (no correspondence) in BT642Year2, they are saved in:
## results/Year2/interestingGeneSets//de_jumps_compareRemapping/leaf_Postflowering_BT642_Day070_vs_Day063_623_Sig_Remap_NotExist.tsv
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.Day070 vs Day063 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 145 71 18 6
## Expressed NotSig 38 20800 2211 1508
## NotExp Exist 3 760 0 x
## NotExist NoCorrespd 6 2093 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 133 62 3 0
## Expressed NotSig 31 19114 1337 0
## NotExp Exist 1 691 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 12 9 15 6
## Expressed NotSig 7 1686 874 1508
## NotExp Exist 2 69 0 x
## NotExist NoCorrespd 6 2093 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 6 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//de_jumps_compareRemapping/root_Postflowering_BT642_Day070_vs_Day063_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 6 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//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 BT642Year2 and log-FC of Year2.
The y-axis is \(M = \text{lfc}_{\text{remap}} - \text{lfc}_{\text{623}}\) and the x-axis is \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), we provide the following histograms to visualize their log fold change values.
Days Jump
Preflowering, Day58 - Day56
Below is the analysis of Day58 vs Day56 from DE_jumps genes between Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day058 vs Day056 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 229 48 38 5
## Expressed NotSig 56 19219 1858 1454
## NotExp Exist 21 651 0 x
## NotExist NoCorrespd 8 1949 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 214 44 20 0
## Expressed NotSig 48 17767 1210 0
## NotExp Exist 17 593 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 15 4 18 5
## Expressed NotSig 8 1452 648 1454
## NotExp Exist 4 58 0 x
## NotExist NoCorrespd 8 1949 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 8 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day058_vs_Day056_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 5 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day058_vs_Day056_623_Sig_Remap_NotExist.tsv
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.Day058 vs Day056 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 4053 240 366 173
## Expressed NotSig 353 16112 2390 1341
## NotExp Exist 126 933 0 x
## NotExist NoCorrespd 265 1834 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 3759 215 149 0
## Expressed NotSig 285 14818 1454 0
## NotExp Exist 115 840 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 294 25 217 173
## Expressed NotSig 68 1294 936 1341
## NotExp Exist 11 93 0 x
## NotExist NoCorrespd 265 1834 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 265 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day058_vs_Day056_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 173 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day058_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 BT642Year2 and log-FC of Year2.
The y-axis is \(M = \text{lfc}_{\text{remap}} - \text{lfc}_{\text{623}}\) and the x-axis is \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), we provide the following histograms to visualize their log fold change values.
Preflowering, Day59 - Day58
Below is the analysis of Day59 vs Day58 from DE_jumps genes between Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day059 vs Day058 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 5 1 0 0
## Expressed NotSig 1 20058 1183 1459
## NotExp Exist 0 159 0 x
## NotExist NoCorrespd 0 1957 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 5 1 0 0
## Expressed NotSig 1 18536 760 0
## NotExp Exist 0 140 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 0 0 0 0
## Expressed NotSig 0 1522 423 1459
## NotExp Exist 0 19 0 x
## NotExist NoCorrespd 0 1957 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 0 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day059_vs_Day058_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 0 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day059_vs_Day058_623_Sig_Remap_NotExist.tsv
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.Day059 vs Day058 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 213 49 53 8
## Expressed NotSig 93 21016 1593 1506
## NotExp Exist 11 435 0 x
## NotExist NoCorrespd 9 2090 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 190 42 24 0
## Expressed NotSig 76 19312 1036 0
## NotExp Exist 10 402 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 23 7 29 8
## Expressed NotSig 17 1704 557 1506
## NotExp Exist 1 33 0 x
## NotExist NoCorrespd 9 2090 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 9 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day059_vs_Day058_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 8 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day059_vs_Day058_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 BT642Year2 and log-FC of Year2.
The y-axis is \(M = \text{lfc}_{\text{remap}} - \text{lfc}_{\text{623}}\) and the x-axis is \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), we provide the following histograms to visualize their log fold change values.
Preflowering, Day61 - Day59
Below is the analysis of Day61 vs Day59 from DE_jumps genes between Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day061 vs Day059 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 1 0 0 1
## Expressed NotSig 0 20088 1163 1458
## NotExp Exist 0 135 0 x
## NotExist NoCorrespd 0 1957 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 1 0 0 0
## Expressed NotSig 0 18565 737 0
## NotExp Exist 0 117 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 0 0 0 1
## Expressed NotSig 0 1523 426 1458
## NotExp Exist 0 18 0 x
## NotExist NoCorrespd 0 1957 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 0 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day061_vs_Day059_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 1 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day061_vs_Day059_623_Sig_Remap_NotExist.tsv
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.Day061 vs Day059 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 137 31 54 6
## Expressed NotSig 26 21237 1576 1508
## NotExp Exist 9 377 0 x
## NotExist NoCorrespd 4 2095 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 110 23 15 0
## Expressed NotSig 17 19539 976 0
## NotExp Exist 7 336 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 27 8 39 6
## Expressed NotSig 9 1698 600 1508
## NotExp Exist 2 41 0 x
## NotExist NoCorrespd 4 2095 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 4 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day061_vs_Day059_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 6 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day061_vs_Day059_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 BT642Year2 and log-FC of Year2.
The y-axis is \(M = \text{lfc}_{\text{remap}} - \text{lfc}_{\text{623}}\) and the x-axis is \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), we provide the following histograms to visualize their log fold change values.
Preflowering, Day63 - Day61
Below is the analysis of Day63 vs Day61 from DE_jumps genes between Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day063 vs Day061 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 0 0 0 1
## Expressed NotSig 1 20073 1176 1458
## NotExp Exist 0 150 0 x
## NotExist NoCorrespd 0 1957 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 0 0 0 0
## Expressed NotSig 1 18554 748 0
## NotExp Exist 0 128 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 0 0 0 1
## Expressed NotSig 0 1519 428 1458
## NotExp Exist 0 22 0 x
## NotExist NoCorrespd 0 1957 x xPlots for numbers of overlapping significant genes：
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 0 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day063_vs_Day061_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 1 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//de_jumps_compareRemapping/leaf_Preflowering_BT642_Day063_vs_Day061_623_Sig_Remap_NotExist.tsv
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.Day063 vs Day061 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 0 0 0 0
## Expressed NotSig 0 21328 1735 1514
## NotExp Exist 0 489 0 x
## NotExist NoCorrespd 0 2099 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 0 0 0 0
## Expressed NotSig 0 19590 1090 0
## NotExp Exist 0 442 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 0 0 0 0
## Expressed NotSig 0 1738 645 1514
## NotExp Exist 0 47 0 x
## NotExist NoCorrespd 0 2099 x xPlots for numbers of overlapping significant genes：
## No significant genes for visualization.
## Save interesting genes (Remap Sig, 623 NotExist):
## ===================================
## We found 0 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day063_vs_Day061_Remap_Sig_623_NotExist.tsv
## Save interesting genes (623 Sig, Remap NotExist):
## ===================================
## We found 0 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//de_jumps_compareRemapping/root_Preflowering_BT642_Day063_vs_Day061_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 BT642Year2 and log-FC of Year2.
The y-axis is \(M = \text{lfc}_{\text{remap}} - \text{lfc}_{\text{623}}\) and the x-axis is \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), we provide the following histograms to visualize their log fold change values.
Postflowering, Day65 - Day63
Below is the analysis of Day65 vs Day63 from DE_jumps genes between Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day065 vs Day063 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 0 0 0 0
## Expressed NotSig 0 20096 1150 1459
## NotExp Exist 0 128 0 x
## NotExist NoCorrespd 0 1957 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 0 0 0 0
## Expressed NotSig 0 18575 728 0
## NotExp Exist 0 108 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 0 0 0 0
## Expressed NotSig 0 1521 422 1459
## NotExp Exist 0 20 0 x
## NotExist NoCorrespd 0 1957 x xPlots for numbers of overlapping significant genes：
## No significant genes for visualization.## No significant genes for visualization.## No significant interesting genes for saving.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.Day065 vs Day063 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 3 0 0 0
## Expressed NotSig 0 21673 1184 1514
## NotExp Exist 1 140 0 x
## NotExist NoCorrespd 0 2099 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 3 0 0 0
## Expressed NotSig 0 19901 776 0
## NotExp Exist 1 127 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 0 0 0 0
## Expressed NotSig 0 1772 408 1514
## NotExp Exist 0 13 0 x
## NotExist NoCorrespd 0 2099 x xPlots for numbers of overlapping significant genes：
## No significant genes for visualization.## No significant interesting genes for saving.Log fold changes of overlapping significant genes
Scatter plots
MA plots
The MA plot visualizes the differences between 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 \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), we provide the following histograms to visualize their log fold change values.
Postflowering, Day68 - Day65
Below is the analysis of Day68 vs Day65 from DE_jumps genes between Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day068 vs Day065 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 0 0 0 0
## Expressed NotSig 0 19230 2191 1459
## NotExp Exist 0 994 0 x
## NotExist NoCorrespd 0 1957 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 0 0 0 0
## Expressed NotSig 0 17738 1565 0
## NotExp Exist 0 945 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 0 0 0 0
## Expressed NotSig 0 1492 626 1459
## NotExp Exist 0 49 0 x
## NotExist NoCorrespd 0 1957 x xPlots for numbers of overlapping significant genes：
## No significant genes for visualization.## No significant genes for visualization.## No significant interesting genes for saving.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.Day068 vs Day065 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 0 0 0 0
## Expressed NotSig 1 21092 2022 1514
## NotExp Exist 0 724 0 x
## NotExist NoCorrespd 0 2099 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 0 0 0 0
## Expressed NotSig 0 19375 1305 0
## NotExp Exist 0 657 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 0 0 0 0
## Expressed NotSig 1 1717 717 1514
## NotExp Exist 0 67 0 x
## NotExist NoCorrespd 0 2099 x xPlots for numbers of overlapping significant genes：
## No significant genes for visualization.## No significant interesting genes for saving.Log fold changes of overlapping significant genes
Scatter plots
MA plots
The MA plot visualizes the differences between 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 \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), we provide the following histograms to visualize their log fold change values.
Day65-Day63, Day66-Day65, Day68-Day66, Day70-Day68
Postflowering, Day70 - Day68
Below is the analysis of Day70 vs Day68 from DE_jumps genes between Year2 and BT642Year2.
Analysis of numbers of overlapping significant genes
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.Day070 vs Day068 : leaf BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 0 0 0 0
## Expressed NotSig 0 19914 1392 1459
## NotExp Exist 0 310 0 x
## NotExist NoCorrespd 0 1957 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 0 0 0 0
## Expressed NotSig 0 18404 899 0
## NotExp Exist 0 279 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 0 0 0 0
## Expressed NotSig 0 1510 493 1459
## NotExp Exist 0 31 0 x
## NotExist NoCorrespd 0 1957 x xPlots for numbers of overlapping significant genes：
## No significant genes for visualization.## No significant genes for visualization.## No significant interesting genes for saving.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.Day070 vs Day068 : root BT642
##
##
##
## Whether (significantly) expressed in both Year2 and BT642Year2 :
## ----------
## For all genes:
## BT642Year2
## Expressed Expressed NotExp NotExist
## Significant NotSig Exist NoCorrespd
## Year2 Expressed Significant 1 5 4 0
## Expressed NotSig 0 21301 1757 1514
## NotExp Exist 0 510 0 x
## NotExist NoCorrespd 0 2099 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 1 4 1 0
## Expressed NotSig 0 19580 1094 0
## NotExp Exist 0 447 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 0 1 3 0
## Expressed NotSig 0 1721 663 1514
## NotExp Exist 0 63 0 x
## NotExist NoCorrespd 0 2099 x xPlots for numbers of overlapping significant genes：
## No significant genes for visualization.## No significant interesting genes for saving.Log fold changes of overlapping significant genes
Scatter plots
MA plots
The MA plot visualizes the differences between 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 \(A = \frac{\text{lfc}_{\text{remap}} + \text{lfc}_{\text{623}}}{2}\) 
Genes only expressend in Year2 or BT642Year2
Since some significantly expressed genes are only expressed in one year, (either Year2 or BT642Year2), we provide the following histograms to visualize their log fold change values.
