Comparison of expression values between year and Year2, root_preflowering
This document has last been compiled on 2021-12-14 23:47:27.
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.
In this file, we compare the raw fpkm counts of samples from root and Preflowering between Year2 and RemapYear2.
Below is the analysis of overlap from the raw fpkm counts between Year2 and BT642Year2:
Load data
Load fpkm counts of all samples
Year2:
## Reading in metadata from file: results/Year2/data/rnaMetaData.txt
## Reading in data from file: results/Year2/data/fpkm_counts.txt## Total number of all samples: 578
## Total number of genes in all samples: 34211
## Removing the 50 samples identified as not part of the main experiment, from the all samples
## After filtering all samples: 528 samples, 34211 genesBT642Year2:
## Reading in metadata from file: results/BT642Year2/data/rnaMetaData.txt
## Reading in data from file: results/BT642Year2/data/fpkm_counts.txt## Total number of all samples: 290
## Total number of genes in all samples: 35115
## Removing the 26 samples identified as not part of the main experiment, from the all samples
## After filtering all samples: 264 samples, 35115 genesFilter samples not in root_preflowering
Year2:
## After filtering: 102 samples, 34211 genesBT642Year2:
## After filtering: 52 samples 35115 genesMatch BTx623 to OrthologGroup
To compare between Year2 and BT642Year2, we need to match the gene naming. In Year2, genes are named with BT623; and in BT642Year2, genes are names with Ortholog Group. So we implemented mapping the BTx623 gene names to the ortholog groups according to the annotation file.
Mapping BTx623 to OrthologGroup:
## Out of 34211 genes with BT623 names,
## 28538 genes are matched to remap gene names.
## Since 0 out of 34056 remap gene names are mapped to multiple BT623 gene names,
## we collapsed on BT623 with average values of counts so that each remap gene has a unique row.## After mapping the BTx623 gene names to the remap gene names,
## Year2 root Preflowering : 102 samples, 34056 genes
## BT642Year2 root Preflowering : 52 samples, 35115 genes
## 
Compare gene expressions in Year2 and BT642Year2
In this section, we will compare the log fpkm counts of genes in Year2 and BT642Year2. Particularly, since there are many samples for each gene, we will use the 3rd max log fpkm counts, the average of log fpkm counts in Day063, and the log log fpkm count from a particular sample of each gene to compare.
There are genes that their counts are results from collapsing and we provide comparison of Year2 and BT642Year2 of these genes. Some genes do not have one-to-one relationship of RT430-to-BT642, so their counts were collapsed by summation when we were merging data from two genotypes. They are flaged as Collasped On Ortholog. Some genes do not have one-to-one relationship of BT623-to-OrthologGroup. so their counts were collapsed by averaging when we were mapping BT623 gene names to ortholog groups. They are flaged as Collapsed on BT623. We also provide analysis that focusing on these genes with collapsed values.
3rd max log expression values
Compare the 3rd max log fpkm counts of genes in Year2 and BT642Year2
Scatter plots
Here are some genes that are only expressed in one year.
10 genes that were expressed in BT642Year2 but not in Year2 (sort by expression vales in BT642Year2):
## GeneID collapsed value_remap value_623 value_diff
## 14751 SbiBTX642.04G091700 1-1 7.204571 0 7.204571
## 13918 SbiBTX642.04G003700 1-1 7.173027 0 7.173027
## 15990 SbiBTX642.04G233300 not1-1 6.218200 0 6.218200
## 15991 SbiBTX642.04G233300 not1-1 6.218200 0 6.218200
## 28764 SbiBTX642.09G172500 1-1 5.702658 0 5.702658
## 30793 SbiBTX642.10G106500 1-1 5.122259 0 5.122259
## 18732 SbiBTX642.05G111600 1-1 4.770300 0 4.770300
## 7769 SbiBTX642.02G264200 1-1 4.738227 0 4.738227
## 16742 SbiBTX642.04G316200 1-1 4.070389 0 4.070389
## 19408 SbiBTX642.05G181900 not1-1 4.053111 0 4.05311110 genes that were expressed in Year2 but not in BT642Year2 (sort by expression vales in Year2):
## 10 genes that were expressed in BT642Year2 but not in Year2 :## GeneID collapsed value_remap value_623 value_diff
## 21025 SbiBTX642.06G103500 1-1 0 7.147714 -7.147714
## 8174 SbiBTX642.02G304600 not1-1 0 6.983108 -6.983108
## 13480 SbiBTX642.03G436300 1-1 0 6.282254 -6.282254
## 1943 SbiBTX642.01G204000 1-1 0 6.194757 -6.194757
## 5447 SbiBTX642.02G010300 1-1 0 5.858230 -5.858230
## 25363 SbiBTX642.08G007300 not1-1 0 5.815832 -5.815832
## 11939 SbiBTX642.03G266300 1-1 0 5.568032 -5.568032
## 7592 SbiBTX642.02G245800 1-1 0 5.113534 -5.113534
## 10553 SbiBTX642.03G104200 1-1 0 4.740928 -4.740928
## 10513 SbiBTX642.03G099500 1-1 0 4.512227 -4.512227Density Plots
Histogram of differences
Mean log expression values in Day63
Compare the average of log fpkm counts of genes in DAY63 in Year2 and BT642Year2
Scatter plots
Here are some genes that are only expressed in one year.
10 genes that were expressed in BT642Year2 but not in Year2 (sort by expression vales in BT642Year2):
## GeneID collapsed value_remap value_623 value_diff
## 13918 SbiBTX642.04G003700 1-1 7.015049 0 7.015049
## 14751 SbiBTX642.04G091700 1-1 6.832446 0 6.832446
## 28764 SbiBTX642.09G172500 1-1 5.250818 0 5.250818
## 18732 SbiBTX642.05G111600 1-1 4.504875 0 4.504875
## 15990 SbiBTX642.04G233300 not1-1 4.331299 0 4.331299
## 15991 SbiBTX642.04G233300 not1-1 4.331299 0 4.331299
## 7769 SbiBTX642.02G264200 1-1 4.247356 0 4.247356
## 15657 SbiBTX642.04G197700 1-1 3.840054 0 3.840054
## 31950 SbiBTX642.10G242600 1-1 3.386647 0 3.386647
## 19408 SbiBTX642.05G181900 not1-1 3.373634 0 3.37363410 genes that were expressed in Year2 but not in BT642Year2 (sort by expression vales in Year2):
## 10 genes that were expressed in BT642Year2 but not in Year2 :## GeneID collapsed value_remap value_623 value_diff
## 13480 SbiBTX642.03G436300 1-1 0 5.690570 -5.690570
## 8174 SbiBTX642.02G304600 not1-1 0 5.552894 -5.552894
## 21025 SbiBTX642.06G103500 1-1 0 5.542046 -5.542046
## 5447 SbiBTX642.02G010300 1-1 0 5.465934 -5.465934
## 11939 SbiBTX642.03G266300 1-1 0 5.029903 -5.029903
## 1943 SbiBTX642.01G204000 1-1 0 4.760238 -4.760238
## 25363 SbiBTX642.08G007300 not1-1 0 4.366161 -4.366161
## 11725 SbiBTX642.03G242600 not1-1 0 3.874339 -3.874339
## 11726 SbiBTX642.03G242600 not1-1 0 3.874339 -3.874339
## 18299 SbiBTX642.05G076400 not1-1 0 3.787112 -3.787112Density Plots
Histogram of differences
Log expression values of a single sample
Compare the log fpkm counts of genes from a single sample in Year2 and BT642Year2
## The randomly selected sample: 0816174R17 from BT642:Day063:Preflowering:RootsScatter plots
Here are some genes that are only expressed in one year.
10 genes that were expressed in BT642Year2 but not in Year2 (sort by expression vales in BT642Year2):
## GeneID collapsed value_remap value_623 value_diff
## 14751 SbiBTX642.04G091700 1-1 6.887160 0 6.887160
## 13918 SbiBTX642.04G003700 1-1 6.829342 0 6.829342
## 28764 SbiBTX642.09G172500 1-1 5.281327 0 5.281327
## 18732 SbiBTX642.05G111600 1-1 4.416164 0 4.416164
## 15990 SbiBTX642.04G233300 not1-1 4.093391 0 4.093391
## 15991 SbiBTX642.04G233300 not1-1 4.093391 0 4.093391
## 2592 SbiBTX642.01G288400 1-1 3.939227 0 3.939227
## 15657 SbiBTX642.04G197700 1-1 3.759156 0 3.759156
## 7769 SbiBTX642.02G264200 1-1 3.720278 0 3.720278
## 16742 SbiBTX642.04G316200 1-1 3.516015 0 3.51601510 genes that were expressed in Year2 but not in BT642Year2 (sort by expression vales in Year2):
## 10 genes that were expressed in BT642Year2 but not in Year2 :## GeneID collapsed value_remap value_623 value_diff
## 13480 SbiBTX642.03G436300 1-1 0 5.905928 -5.905928
## 8174 SbiBTX642.02G304600 not1-1 0 5.633431 -5.633431
## 21025 SbiBTX642.06G103500 1-1 0 5.389911 -5.389911
## 5447 SbiBTX642.02G010300 1-1 0 5.274262 -5.274262
## 11939 SbiBTX642.03G266300 1-1 0 5.033863 -5.033863
## 1943 SbiBTX642.01G204000 1-1 0 4.721373 -4.721373
## 23726 SbiBTX642.07G071400 not1-1 0 3.915052 -3.915052
## 23727 SbiBTX642.07G071400 not1-1 0 3.915052 -3.915052
## 23595 SbiBTX642.07G055600 not1-1 0 3.670161 -3.670161
## 6612 SbiBTX642.02G125300 not1-1 0 3.637960 -3.637960Density Plots
Histogram of differences
