Chapter 3: Results
3.4 Bioinformatics Analysis
3.4.1 Analysis of Transcriptome
Figure 12: PCA of samples. I. aquatica leaves (top left), and roots (top right). I. pes- caprae leaves (bottom left), and roots (bottom right).
Differential gene analysis using DESeq2 results as well as analysis of the enriched pathways are shown in the Figures below. Figure 13 shows the numbers of up- and downregulated genes in I. aquatica and I. pes-caprae leaf samples and Figure 14 represents the differentially expressed genes for the root samples, in all stages of the experiment. The differential expression analysis of genes was achieved by three pairs of comparisons: Early and Control samples, Late and Control samples, as well as Late and Early samples. Genes from the Early and Late samples were compared to Control to identify the absolute differential expression in these samples. Then, the Late and Early samples were compared to study the expression profiles of genes throughout the experiment.
For example, a Bet-domain containing protein (pfam: PF00407) was found to be differentially expressed in the leaves of I. aquatica. This gene downregulated 7 folds in the Early samples, but the expression was found to be neutral in the Late sample (0.8 fold change). When comparing the Late to Early samples, the fold change of this gene is determined to be upregulated by 8.5 folds. Thus, looking at the differential expression of genes in all three pairs of comparisons gives a more comprehensive understanding of the expression profile of a gene.
28 Figure 13: Differential gene expression analysis of Leaf samples from I. aquatica and I. pes-caprae. The figures show the numbers of
differentially expressed genes in the Leaf in Early and Late samples compared to the Control samples, as well as Late sample compared to Early sample. The scatter plots on the left represent all genes, and the bar graphs on the right represent the number of genes up- and downregulated in each sample.
29 Figure 14: Differential gene expression analysis of Root samples from I. aquatica and I. pes-caprae. The figures show the numbers of
differentially expressed genes in the Root in Early and Late samples compared to the Control samples, as well as Late sample compared to Early sample. The scatter plots on the left represent all genes, and the bar graphs on the right represent the number of genes up- and downregulated in each sample.
The functional annotation of genes in all samples was performed to determine the pfam accession and KO identifier associated with each gene based on their nucleotide sequence. These accessions were then used to study the pathways enriched in samples during salt-stress. The dcGO Enrichment online tool was used to identify the enrichment of pathways related to cellular components, biological processes, and molecular functions. Then, RStudio was used to visualize the up- and downregulated pathways (Figures 15-18). Pathways that are related to salinity-stress were identified and studied further to determine the fold changes of these pathways in all samples (Figures 19-20).
Analysis of leaf samples of I. aquatica and I. pes-caprae revealed several interesting pathways. I. aquatica leaves showed downregulation of photosynthesis related pathways (Figures 15 & 19). It also showed upregulation of abiotic-stress related pathways, while downregulation of other (Figures 15 & 19 ). However, I. pes- caprae leaves demonstrated upregulation of salt-stress related pathways as well as water depravation pathways (Figures 17 &19). The latter was upregulated by 2-4 folds in the Early samples (Figure 19). Since, salt stress leads to an increase of reactive oxygen species in cells, it is expected to detect upregulation of oxidoreduction related pathways. However, I. aquatica leaves showed little difference in the expression of oxidoreduction related pathways (Figures 15 & 19). On the other hand, I. pes-caprae demonstrated upregulation of pathways related to oxidoreduction, response to reactive oxygen species, and oxidoreduction coenzyme metabolic pathways (Figures 17 & 19).
To maintain cellular homeostasis during salinity stress, plants utilize ion transport pathways, which is evident in I. pes-caprae leaves. I. pes-caprae displayed high expressed of pathways related to ion transport in all samples even Control (Figure 19).
However, I. aquatica leaves show downregulation of ion/anion transport pathways in the Early samples, followed by upregulation in Late samples only (Figure 19).
Analysis of root samples of I. aquatica and I. pes-caprae revealed some interesting pathways. In I. aquatica roots, there was some upregulation of pathways related to water depravation and osmotic stress in the Early samples followed by downregulation of these pathways in the Late samples (Figures 16 & 20). I. pes-caprae root showed higher upregulation of pathways related to salt and osmotic stress, especially in the Early samples (2-4 folds upregulation) (Figure 20). Pathways related to reactive oxygen species were found to be upregulated in both plants; however, the fold changes were higher in I. pes-caprae root sample (Figures 17, 18, & 20). I.
aquatica roots were found to upregulate several pathways related to transcription and RNA processing in the Late samples. This could be an indication that I. aquatica roots have a latent response to salinity compared to I. pes-caprae. Another interesting finding was the changes in expression of lipid-related pathways in both plants. During salt-stress, the increase of reactive oxygen species leads to the oxidation of some membrane lipids, which in turn damages the membrane fluidity and cell structure (Natera et al., 2016; Yu et al., 2020). Pathways related to lipid metabolism were upregulated in I. pes-caprae roots (all sample) but downregulated in I. aquatica roots Early sample (Figures 17, 18, & 20). Further analysis into the specific lipids and pathways that are differentially expressed between I. aquatica and I. pes-caprae can further clarify the differences in salt-tolerance of these plants. The analysis of pathways sheds light on many aspects of salt-tolerance that can be examined in more detail in future research.
32 Early versus Control Late versus Control Late versus Early
Figure 15: Differential expression of pathways in I. aquatica leaves. Both KO (from KEGG) and pfam (from Uniprot/EMBL-EBI) were determined for each gene then dcGO tool was used to determine all enriched pathways. The diagram shows the up- and downregulated pathways in all samples.
33 Early versus Control Late versus Control Late versus Early
Figure 16: Differential expression of pathways in I. aquatica roots. Both KO (from KEGG) and pfam (from Uniprot/EMBL-EBI) were determined for each gene then dcGO tool was used to determine all enriched pathways. The diagram shows the up- and downregulated pathways in all samples.
34 Early versus Control Late versus Control Late versus Early
Figure 17: Differential expression of pathways in I. pes-caprae leaves. Both KO (from KEGG) and pfam (from Uniprot/EMBL-EBI) were determined for each gene then dcGO tool was used to determine all enriched pathways. The diagram shows the up- and
downregulated pathways in all samples.
35
Early versus Control Late versus Control Late versus Early
Figure 18: Differential expression of pathways in I. pes-caprae roots. Both KO (from KEGG) and pfam (from Uniprot/EMBL-EBI)
were determined for each gene then dcGO tool was used to determine all enriched pathways. The diagram shows the up- and downregulated pathways in all samples.
36 Figure 19: Differential gene expression of salt related identified pathways in Leaf samples. The heatmap represents the salt-related
differentially expressed pathways in all samples (Control, Early and Late) in Leaf tissues.
CL1 CL2 CL3 EL1 EL2 EL3 LL1 LL2 LL3
2.54e-05 Cellular macromolecule biosynthetic process 3.25e-05 Macromolecule biosynthetic process
3.04e-05 Cellular nitrogen compound biosynthetic process 2.54e-05 Phosphorus metabolic process
3.18e-05 Phosphate-containing compound metabolic process 2.54e-05 Regulation of translation
3.25e-05 de novo protein folding 3.25e-05 Ion transport
2.54e-05 Regulation of cellular amide metabolic process 2.54e-05 Defense response to fungus
2.54e-05 Anion transport
2.54e-05 Iron-sulfur cluster assembly 2.54e-05 Metallo-sulfur cluster assembly 2.54e-05 Cellular response to antibiotic
3.25e-05 Posttranscriptional regulation of gene expression 3.25e-05 Programmed cell death
2.54e-05 Cellular response to drug 3.25e-05 Cell death
3.25e-05 Activation of innate immune response 3.25e-05 Activation of immune response 2.54e-05 Chaperone-mediated protein folding 2.54e-05 Purine ribonucleoside metabolic process 3.25e-05 S-glycoside metabolic process 2.54e-05 Heme metabolic process 2.54e-05 Heme biosynthetic process 2.54e-05 Systemic acquired resistance
2.54e-05 Defense response to fungus, incompatible interaction 2.54e-05 Inorganic ion homeostasis
3.25e-05 Glycerol metabolic process
3.25e-05 Alditol metabolic process CR1 CR2 CR3 ER1 ER2 ER3 LR1 LR2 LR3
1.06e-03 Positive regulation of transcription, DNA-templated 9.49e-04 Positive regulation of RNA biosynthetic process 9.49e-04 Positive regulation of nucleic acid-templated transcription 9.49e-04 Positive regulation of RNA metabolic process
9.49e-04 Isoprenoid biosynthetic process 1.55e-03 Isoprenoid metabolic process
5.27e-04 Positive regulation of cellular biosynthetic process 5.27e-04 Positive regulation of biosynthetic process
9.49e-04 Positive regulation of nucleobase-containing compound 5.27e-04 Positive regulation of macromolecule biosynthetic process 2.35e-03 Glutamine metabolic process
5.27e-04 Positive regulation of gene expression 3.09e-03 Terpenoid biosynthetic process 9.49e-04 DNA-templated transcription, termination
8.60e-04 Positive regulation of nitrogen compound metabolic process 9.49e-04 Positive regulation of cellular metabolic process
9.49e-04 Positive regulation of metabolic process 1.33e-03 Starch metabolic process
3.03e-03 Regulation of cellular response to stress
9.49e-04 Positive regulation of transcription in response to stress 9.49e-04 Positive regulation of transcription in response to heat stress 1.23e-03 Positive regulation of macromolecule metabolic process 1.40e-03 Heat acclimation
3.09e-03 Regulation of DNA-templated transcription in response to stress 2.96e-03 Starch biosynthetic process
2.65e-03 Regulation of transcription in response to stress 2.35e-03 Nucleotide-sugar metabolic process
3.09e-03 Nucleotide-sugar biosynthetic process
3.09e-03 Cellular response to topologically incorrect protein 1.55e-03 Regulation of response to osmotic stress
CL1 CL2 CL3 EL1 EL2 EL3 LL1 LL3
5.23e-03 Cytoplasmic translation
4.44e-03 Response to oxygen-containing compound 4.44e-03 Response to acid chemical
5.23e-03 Response to chemical 5.23e-03 Coenzyme biosynthetic process
5.23e-03 Nicotinamide nucleotide biosynthetic process 5.23e-03 Nucleoside diphosphate phosphorylation 5.23e-03 Response to water deprivation 5.23e-03 Response to water
5.23e-03 Nucleoside diphosphate metabolic process 5.23e-03 Polysaccharide catabolic process 5.23e-03 Response to organic substance 5.23e-03 Organic acid catabolic process 5.23e-03 Response to lipid
5.23e-03 Mitochondrial ATP synthesis coupled electron transport 5.23e-03 Oxidoreduction coenzyme metabolic process 4.44e-03 Pyruvate metabolic process
5.23e-03 Glucose metabolic process
5.23e-03 Pyridine nucleotide metabolic process 5.23e-03 Regulation of cell communication 5.23e-03 Response to reactive oxygen species 5.23e-03 Regulation of signal transduction 5.23e-03 Regulation of signaling
5.23e-03 Adaxial/abaxial pattern specification 5.23e-03 Jasmonic acid biosynthetic process 5.23e-03 Regulation of photomorphogenesis 5.23e-03 Cellular iron ion homeostasis 4.44e-03 L-phenylalanine metabolic process
4.44e-03 Erythrose 4-phosphate/phosphoenolpyruvate family 5.23e-03 Manganese ion transport
-8
-6
-4
-2
0
2
4 CR1 CR2 CR3 ER1 ER2 ER3 LR1 LR2 LR3
1.43e-04 Movement of cell or subcellular component 8.63e-05 Organelle organization
1.58e-04 Cytoplasmic microtubule organization 4.67e-05 Cortical microtubule organization 6.39e-05 Autophagy
6.39e-05 Process utilizing autophagic mechanism 5.70e-05 Response to salt stress
1.58e-04 Regulation of microtubule-based process 5.70e-05 Response to osmotic stress
1.33e-04 Phosphorelay signal transduction system 4.67e-05 Ethylene-activated signaling pathway 6.39e-05 Cellular lipid catabolic process
1.24e-04 Nucleoside triphosphate biosynthetic process 6.39e-05 Ribonucleoside triphosphate biosynthetic process 1.58e-04 Purine nucleoside triphosphate biosynthetic process 1.58e-04 Purine ribonucleoside triphosphate iosynthetic process 6.39e-05 Sphingolipid metabolic process
4.67e-05 Defense response to fungus 1.58e-04 DNA-templated transcription, initiation 5.70e-05 Regulation of circadian rhythm 4.67e-05 Ethylene metabolic process 4.67e-05 Ethylene biosynthetic process 4.67e-05 Cellular alkene metabolic process 4.67e-05 Alkene biosynthetic process 4.67e-05 Olefin metabolic process 4.67e-05 Olefin biosynthetic process 1.49e-04 Regulation of transferase activity 5.70e-05 Diterpenoid biosynthetic process 1.58e-04 Membrane lipid metabolic process 4.67e-05 Diterpenoid metabolic process
I.pes-caprae leaf I.pes-caprae root
CL1 CL2 CL3 EL1 EL2 EL3 LL1 LL2 LL3
2.54e-05 Cellular macromolecule biosynthetic process 3.25e-05 Macromolecule biosynthetic process
3.04e-05 Cellular nitrogen compound biosynthetic process 2.54e-05 Phosphorus metabolic process
3.18e-05 Phosphate-containing compound metabolic process 2.54e-05 Regulation of translation
3.25e-05 de novo protein folding 3.25e-05 Ion transport
2.54e-05 Regulation of cellular amide metabolic process 2.54e-05 Defense response to fungus
2.54e-05 Anion transport
2.54e-05 Iron-sulfur cluster assembly 2.54e-05 Metallo-sulfur cluster assembly 2.54e-05 Cellular response to antibiotic
3.25e-05 Posttranscriptional regulation of gene expression 3.25e-05 Programmed cell death
2.54e-05 Cellular response to drug 3.25e-05 Cell death
3.25e-05 Activation of innate immune response 3.25e-05 Activation of immune response 2.54e-05 Chaperone-mediated protein folding 2.54e-05 Purine ribonucleoside metabolic process 3.25e-05 S-glycoside metabolic process 2.54e-05 Heme metabolic process 2.54e-05 Heme biosynthetic process 2.54e-05 Systemic acquired resistance
2.54e-05 Defense response to fungus, incompatible interaction 2.54e-05 Inorganic ion homeostasis
3.25e-05 Glycerol metabolic process 3.25e-05 Alditol metabolic process
-5
0
5 CR1 CR2 CR3 ER1 ER2 ER3 LR1 LR2 LR3
1.06e-03 Positive regulation of transcription, DNA-templated 9.49e-04 Positive regulation of RNA biosynthetic process 9.49e-04 Positive regulation of nucleic acid-templated transcription 9.49e-04 Positive regulation of RNA metabolic process
9.49e-04 Isoprenoid biosynthetic process 1.55e-03 Isoprenoid metabolic process
5.27e-04 Positive regulation of cellular biosynthetic process 5.27e-04 Positive regulation of biosynthetic process
9.49e-04 Positive regulation of nucleobase-containing compound 5.27e-04 Positive regulation of macromolecule biosynthetic process 2.35e-03 Glutamine metabolic process
5.27e-04 Positive regulation of gene expression 3.09e-03 Terpenoid biosynthetic process 9.49e-04 DNA-templated transcription, termination
8.60e-04 Positive regulation of nitrogen compound metabolic process 9.49e-04 Positive regulation of cellular metabolic process
9.49e-04 Positive regulation of metabolic process 1.33e-03 Starch metabolic process
3.03e-03 Regulation of cellular response to stress
9.49e-04 Positive regulation of transcription in response to stress 9.49e-04 Positive regulation of transcription in response to heat stress 1.23e-03 Positive regulation of macromolecule metabolic process 1.40e-03 Heat acclimation
3.09e-03 Regulation of DNA-templated transcription in response to stress 2.96e-03 Starch biosynthetic process
2.65e-03 Regulation of transcription in response to stress 2.35e-03 Nucleotide-sugar metabolic process
3.09e-03 Nucleotide-sugar biosynthetic process
3.09e-03 Cellular response to topologically incorrect protein 1.55e-03 Regulation of response to osmotic stress
I.aquatica leaf I.aquatica root
CL1 CL2 CL3 EL1 EL2 EL3 LL1 LL3
5.23e-03 Cytoplasmic translation
4.44e-03 Response to oxygen-containing compound 4.44e-03 Response to acid chemical
5.23e-03 Response to chemical 5.23e-03 Coenzyme biosynthetic process
5.23e-03 Nicotinamide nucleotide biosynthetic process 5.23e-03 Nucleoside diphosphate phosphorylation 5.23e-03 Response to water deprivation 5.23e-03 Response to water
5.23e-03 Nucleoside diphosphate metabolic process 5.23e-03 Polysaccharide catabolic process 5.23e-03 Response to organic substance 5.23e-03 Organic acid catabolic process 5.23e-03 Response to lipid
5.23e-03 Mitochondrial ATP synthesis coupled electron transport 5.23e-03 Oxidoreduction coenzyme metabolic process 4.44e-03 Pyruvate metabolic process
5.23e-03 Glucose metabolic process 5.23e-03 Pyridine nucleotide metabolic process 5.23e-03 Regulation of cell communication 5.23e-03 Response to reactive oxygen species 5.23e-03 Regulation of signal transduction 5.23e-03 Regulation of signaling
5.23e-03 Adaxial/abaxial pattern specification 5.23e-03 Jasmonic acid biosynthetic process 5.23e-03 Regulation of photomorphogenesis 5.23e-03 Cellular iron ion homeostasis 4.44e-03 L-phenylalanine metabolic process
4.44e-03 Erythrose 4-phosphate/phosphoenolpyruvate family
5.23e-03 Manganese ion transport CR1 CR2 CR3 ER1 ER2 ER3 LR1 LR2 LR3
1.43e-04 Movement of cell or subcellular component 8.63e-05 Organelle organization
1.58e-04 Cytoplasmic microtubule organization 4.67e-05 Cortical microtubule organization 6.39e-05 Autophagy
6.39e-05 Process utilizing autophagic mechanism 5.70e-05 Response to salt stress
1.58e-04 Regulation of microtubule-based process 5.70e-05 Response to osmotic stress
1.33e-04 Phosphorelay signal transduction system 4.67e-05 Ethylene-activated signaling pathway 6.39e-05 Cellular lipid catabolic process
1.24e-04 Nucleoside triphosphate biosynthetic process 6.39e-05 Ribonucleoside triphosphate biosynthetic process 1.58e-04 Purine nucleoside triphosphate biosynthetic process 1.58e-04 Purine ribonucleoside triphosphate iosynthetic process 6.39e-05 Sphingolipid metabolic process
4.67e-05 Defense response to fungus 1.58e-04 DNA-templated transcription, initiation 5.70e-05 Regulation of circadian rhythm 4.67e-05 Ethylene metabolic process 4.67e-05 Ethylene biosynthetic process 4.67e-05 Cellular alkene metabolic process 4.67e-05 Alkene biosynthetic process 4.67e-05 Olefin metabolic process 4.67e-05 Olefin biosynthetic process 1.49e-04 Regulation of transferase activity 5.70e-05 Diterpenoid biosynthetic process 1.58e-04 Membrane lipid metabolic process 4.67e-05 Diterpenoid metabolic process
I.pes-caprae leaf I.pes-caprae root
37 Figure 20: Differential gene expression of salt related identified pathways in Root samples. The heatmap represents the salt-related differentially expressed pathways in all samples (Control, Early and Late) in Root tissues.
CL1 CL2 CL3 EL1 EL2 EL3 LL1 LL2 LL3
2.54e-05 Cellular macromolecule biosynthetic process 3.25e-05 Macromolecule biosynthetic process
3.04e-05 Cellular nitrogen compound biosynthetic process 2.54e-05 Phosphorus metabolic process
3.18e-05 Phosphate-containing compound metabolic process 2.54e-05 Regulation of translation
3.25e-05 de novo protein folding 3.25e-05 Ion transport
2.54e-05 Regulation of cellular amide metabolic process 2.54e-05 Defense response to fungus
2.54e-05 Anion transport
2.54e-05 Iron-sulfur cluster assembly 2.54e-05 Metallo-sulfur cluster assembly 2.54e-05 Cellular response to antibiotic
3.25e-05 Posttranscriptional regulation of gene expression 3.25e-05 Programmed cell death
2.54e-05 Cellular response to drug 3.25e-05 Cell death
3.25e-05 Activation of innate immune response 3.25e-05 Activation of immune response 2.54e-05 Chaperone-mediated protein folding 2.54e-05 Purine ribonucleoside metabolic process 3.25e-05 S-glycoside metabolic process 2.54e-05 Heme metabolic process 2.54e-05 Heme biosynthetic process 2.54e-05 Systemic acquired resistance
2.54e-05 Defense response to fungus, incompatible interaction 2.54e-05 Inorganic ion homeostasis
3.25e-05 Glycerol metabolic process
3.25e-05 Alditol metabolic process CR1 CR2 CR3 ER1 ER2 ER3 LR1 LR2 LR3
1.06e-03 Positive regulation of transcription, DNA-templated 9.49e-04 Positive regulation of RNA biosynthetic process 9.49e-04 Positive regulation of nucleic acid-templated transcription 9.49e-04 Positive regulation of RNA metabolic process
9.49e-04 Isoprenoid biosynthetic process 1.55e-03 Isoprenoid metabolic process
5.27e-04 Positive regulation of cellular biosynthetic process 5.27e-04 Positive regulation of biosynthetic process
9.49e-04 Positive regulation of nucleobase-containing compound 5.27e-04 Positive regulation of macromolecule biosynthetic process 2.35e-03 Glutamine metabolic process
5.27e-04 Positive regulation of gene expression 3.09e-03 Terpenoid biosynthetic process 9.49e-04 DNA-templated transcription, termination
8.60e-04 Positive regulation of nitrogen compound metabolic process 9.49e-04 Positive regulation of cellular metabolic process
9.49e-04 Positive regulation of metabolic process 1.33e-03 Starch metabolic process
3.03e-03 Regulation of cellular response to stress
9.49e-04 Positive regulation of transcription in response to stress 9.49e-04 Positive regulation of transcription in response to heat stress 1.23e-03 Positive regulation of macromolecule metabolic process 1.40e-03 Heat acclimation
3.09e-03 Regulation of DNA-templated transcription in response to stress 2.96e-03 Starch biosynthetic process
2.65e-03 Regulation of transcription in response to stress 2.35e-03 Nucleotide-sugar metabolic process
3.09e-03 Nucleotide-sugar biosynthetic process
3.09e-03 Cellular response to topologically incorrect protein 1.55e-03 Regulation of response to osmotic stress
-4
-2
0
2
4
I.aquatica leaf I.aquatica root
CL1 CL2 CL3 EL1 EL2 EL3 LL1 LL3
5.23e-03 Cytoplasmic translation
4.44e-03 Response to oxygen-containing compound 4.44e-03 Response to acid chemical
5.23e-03 Response to chemical 5.23e-03 Coenzyme biosynthetic process
5.23e-03 Nicotinamide nucleotide biosynthetic process 5.23e-03 Nucleoside diphosphate phosphorylation 5.23e-03 Response to water deprivation 5.23e-03 Response to water
5.23e-03 Nucleoside diphosphate metabolic process 5.23e-03 Polysaccharide catabolic process 5.23e-03 Response to organic substance 5.23e-03 Organic acid catabolic process 5.23e-03 Response to lipid
5.23e-03 Mitochondrial ATP synthesis coupled electron transport 5.23e-03 Oxidoreduction coenzyme metabolic process 4.44e-03 Pyruvate metabolic process
5.23e-03 Glucose metabolic process 5.23e-03 Pyridine nucleotide metabolic process 5.23e-03 Regulation of cell communication 5.23e-03 Response to reactive oxygen species 5.23e-03 Regulation of signal transduction 5.23e-03 Regulation of signaling
5.23e-03 Adaxial/abaxial pattern specification 5.23e-03 Jasmonic acid biosynthetic process 5.23e-03 Regulation of photomorphogenesis 5.23e-03 Cellular iron ion homeostasis 4.44e-03 L-phenylalanine metabolic process
4.44e-03 Erythrose 4-phosphate/phosphoenolpyruvate family
5.23e-03 Manganese ion transport CR1 CR2 CR3 ER1 ER2 ER3 LR1 LR2 LR3
1.43e-04 Movement of cell or subcellular component 8.63e-05 Organelle organization
1.58e-04 Cytoplasmic microtubule organization 4.67e-05 Cortical microtubule organization 6.39e-05 Autophagy
6.39e-05 Process utilizing autophagic mechanism 5.70e-05 Response to salt stress
1.58e-04 Regulation of microtubule-based process 5.70e-05 Response to osmotic stress
1.33e-04 Phosphorelay signal transduction system 4.67e-05 Ethylene-activated signaling pathway 6.39e-05 Cellular lipid catabolic process
1.24e-04 Nucleoside triphosphate biosynthetic process 6.39e-05 Ribonucleoside triphosphate biosynthetic process 1.58e-04 Purine nucleoside triphosphate biosynthetic process 1.58e-04 Purine ribonucleoside triphosphate iosynthetic process 6.39e-05 Sphingolipid metabolic process
4.67e-05 Defense response to fungus 1.58e-04 DNA-templated transcription, initiation 5.70e-05 Regulation of circadian rhythm 4.67e-05 Ethylene metabolic process 4.67e-05 Ethylene biosynthetic process 4.67e-05 Cellular alkene metabolic process 4.67e-05 Alkene biosynthetic process 4.67e-05 Olefin metabolic process 4.67e-05 Olefin biosynthetic process 1.49e-04 Regulation of transferase activity 5.70e-05 Diterpenoid biosynthetic process 1.58e-04 Membrane lipid metabolic process 4.67e-05 Diterpenoid metabolic process
I.pes-caprae leaf I.pes-caprae root
CL1 CL2 CL3 EL1 EL2 EL3 LL1 LL2 LL3
2.54e-05 Cellular macromolecule biosynthetic process 3.25e-05 Macromolecule biosynthetic process
3.04e-05 Cellular nitrogen compound biosynthetic process 2.54e-05 Phosphorus metabolic process
3.18e-05 Phosphate-containing compound metabolic process 2.54e-05 Regulation of translation
3.25e-05 de novo protein folding 3.25e-05 Ion transport
2.54e-05 Regulation of cellular amide metabolic process 2.54e-05 Defense response to fungus
2.54e-05 Anion transport
2.54e-05 Iron-sulfur cluster assembly 2.54e-05 Metallo-sulfur cluster assembly 2.54e-05 Cellular response to antibiotic
3.25e-05 Posttranscriptional regulation of gene expression 3.25e-05 Programmed cell death
2.54e-05 Cellular response to drug 3.25e-05 Cell death
3.25e-05 Activation of innate immune response 3.25e-05 Activation of immune response 2.54e-05 Chaperone-mediated protein folding 2.54e-05 Purine ribonucleoside metabolic process 3.25e-05 S-glycoside metabolic process 2.54e-05 Heme metabolic process 2.54e-05 Heme biosynthetic process 2.54e-05 Systemic acquired resistance
2.54e-05 Defense response to fungus, incompatible interaction 2.54e-05 Inorganic ion homeostasis
3.25e-05 Glycerol metabolic process
3.25e-05 Alditol metabolic process CR1 CR2 CR3 ER1 ER2 ER3 LR1 LR2 LR3
1.06e-03 Positive regulation of transcription, DNA-templated 9.49e-04 Positive regulation of RNA biosynthetic process 9.49e-04 Positive regulation of nucleic acid-templated transcription 9.49e-04 Positive regulation of RNA metabolic process
9.49e-04 Isoprenoid biosynthetic process 1.55e-03 Isoprenoid metabolic process
5.27e-04 Positive regulation of cellular biosynthetic process 5.27e-04 Positive regulation of biosynthetic process
9.49e-04 Positive regulation of nucleobase-containing compound 5.27e-04 Positive regulation of macromolecule biosynthetic process 2.35e-03 Glutamine metabolic process
5.27e-04 Positive regulation of gene expression 3.09e-03 Terpenoid biosynthetic process 9.49e-04 DNA-templated transcription, termination
8.60e-04 Positive regulation of nitrogen compound metabolic process 9.49e-04 Positive regulation of cellular metabolic process
9.49e-04 Positive regulation of metabolic process 1.33e-03 Starch metabolic process
3.03e-03 Regulation of cellular response to stress
9.49e-04 Positive regulation of transcription in response to stress 9.49e-04 Positive regulation of transcription in response to heat stress 1.23e-03 Positive regulation of macromolecule metabolic process 1.40e-03 Heat acclimation
3.09e-03 Regulation of DNA-templated transcription in response to stress 2.96e-03 Starch biosynthetic process
2.65e-03 Regulation of transcription in response to stress 2.35e-03 Nucleotide-sugar metabolic process
3.09e-03 Nucleotide-sugar biosynthetic process
3.09e-03 Cellular response to topologically incorrect protein 1.55e-03 Regulation of response to osmotic stress
CL1 CL2 CL3 EL1 EL2 EL3 LL1 LL3
5.23e-03 Cytoplasmic translation
4.44e-03 Response to oxygen-containing compound 4.44e-03 Response to acid chemical
5.23e-03 Response to chemical 5.23e-03 Coenzyme biosynthetic process
5.23e-03 Nicotinamide nucleotide biosynthetic process 5.23e-03 Nucleoside diphosphate phosphorylation 5.23e-03 Response to water deprivation 5.23e-03 Response to water
5.23e-03 Nucleoside diphosphate metabolic process 5.23e-03 Polysaccharide catabolic process 5.23e-03 Response to organic substance 5.23e-03 Organic acid catabolic process 5.23e-03 Response to lipid
5.23e-03 Mitochondrial ATP synthesis coupled electron transport 5.23e-03 Oxidoreduction coenzyme metabolic process 4.44e-03 Pyruvate metabolic process
5.23e-03 Glucose metabolic process 5.23e-03 Pyridine nucleotide metabolic process 5.23e-03 Regulation of cell communication 5.23e-03 Response to reactive oxygen species 5.23e-03 Regulation of signal transduction 5.23e-03 Regulation of signaling
5.23e-03 Adaxial/abaxial pattern specification 5.23e-03 Jasmonic acid biosynthetic process 5.23e-03 Regulation of photomorphogenesis 5.23e-03 Cellular iron ion homeostasis 4.44e-03 L-phenylalanine metabolic process
4.44e-03 Erythrose 4-phosphate/phosphoenolpyruvate family
5.23e-03 Manganese ion transport CR1 CR2 CR3 ER1 ER2 ER3 LR1 LR2 LR3
1.43e-04 Movement of cell or subcellular component 8.63e-05 Organelle organization
1.58e-04 Cytoplasmic microtubule organization 4.67e-05 Cortical microtubule organization 6.39e-05 Autophagy
6.39e-05 Process utilizing autophagic mechanism 5.70e-05 Response to salt stress
1.58e-04 Regulation of microtubule-based process 5.70e-05 Response to osmotic stress
1.33e-04 Phosphorelay signal transduction system 4.67e-05 Ethylene-activated signaling pathway 6.39e-05 Cellular lipid catabolic process
1.24e-04 Nucleoside triphosphate biosynthetic process 6.39e-05 Ribonucleoside triphosphate biosynthetic process 1.58e-04 Purine nucleoside triphosphate biosynthetic process 1.58e-04 Purine ribonucleoside triphosphate iosynthetic process 6.39e-05 Sphingolipid metabolic process
4.67e-05 Defense response to fungus 1.58e-04 DNA-templated transcription, initiation 5.70e-05 Regulation of circadian rhythm 4.67e-05 Ethylene metabolic process 4.67e-05 Ethylene biosynthetic process 4.67e-05 Cellular alkene metabolic process 4.67e-05 Alkene biosynthetic process 4.67e-05 Olefin metabolic process 4.67e-05 Olefin biosynthetic process 1.49e-04 Regulation of transferase activity 5.70e-05 Diterpenoid biosynthetic process 1.58e-04 Membrane lipid metabolic process 4.67e-05 Diterpenoid metabolic process
-5
0
5
I.pes-caprae leaf I.pes-caprae root