Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight
Abstract
:1. Introduction
2. Materials and Methods
2.1. GeneLab Datasets
2.2. Gene Regulatory Network Inferencing Using Pearson Correlation
2.3. Causal Relations Discovery Using Incremental Association Markov Blanket (IAMB) Method
2.4. Computation of Network Measures
2.5. Logistic Regression-Based Gene Ranking
3. Results
3.1. Cellular Response to Stimulus
3.2. Cellular Response to Stress
3.3. Cellular Response to DNA Damage Stimulus
3.4. DNA Metabolic Process
3.5. Flavonoid Biosynthesis and Carotenoid Catabolic Processes
3.6. Subnetwork Measurments for the Low, and Very High Radiation Dose DDR Processes
3.7. Jaccard Similarity Between Subnetworks
3.8. Logistic Regression Ranking of Hub Genes
3.9. Causal Relational Network Analysis
4. Discussion
4.1. Computational Strategy
4.2. ATR/ATM Gene Interactions
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Arabidopsis Gene Identifier for Hub Genes | Degree Distribution | Subgraph Centrality | ||
---|---|---|---|---|
LRD1 | LRD2 | LRD1 | LRD2 | |
AT1G08260 | 1 | 1 | 1.5431 | 1.5431 |
AT1G29440 | 1 | 1 | 1.5431 | 1.5431 |
AT2G30360 | 1 | 4 | 1.5431 | 1.5431 |
AT3G13380 | 12 | 7 | 15.9895 | 7.0825 |
AT3G51920 | 6 | 1 | 5.8344 | 1.5431 |
AT3G61630 | 2 | 13 | 2.1782 | 18.4146 |
AT4G28950 | 1 | 3 | 1.5431 | 2.9146 |
AT5G07100 | 1 | 9 | 1.5431 | 10.0677 |
AT5G40840 | 4 | 4 | 3.7622 | 3.7622 |
AT5G48720 | 1 | 20 | 1.5431 | 3.7622 |
AT5G61600 | 1 | 15 | 2.1782 | 18.4146 |
Arabidopsis Gene Identifier for Hub Genes | Degree Distribution | Subgraph Centrality | ||
---|---|---|---|---|
LRD3 | LRD4 | LRD3 | LRD4 | |
AT3G27060 | 2 | 22 | 2.3811 | 6253.2089 |
AT3G51920 | 4 | 40 | 4.9976 | 11,529.486 |
AT1G70940 | 1 | 22 | 1.5907 | 12,412.744 |
Arabidopsis Gene Identifier for Hub Genes | Degree Distribution | Subgraph Centrality | ||
---|---|---|---|---|
LRD1 | LRD2 | LRD1 | LRD2 | |
AT1G08260 | 1 | 1 | 1.5431 | 1.5431 |
AT5G40840 | 4 | 4 | 3.7622 | 3.7622 |
AT5G07100 | 1 | 9 | 1.5431 | 10.0677 |
AT5G48720 | 1 | 20 | 1.5431 | 43.7775 |
DDR Processes | Degree Distribution | Subgraph Centrality | ||
---|---|---|---|---|
LRD3 | LRD4 | LRD3 | LRD4 | |
Cellular response to stress | 3 | 22 | 54.4538 | 2.9737 |
Cellular response to DNA damage stimulus | 2 | 33 | 2.1782 | 156.2451 |
DNA metabolic process | 2 | 22 | 2.3811 | 57.2840 |
Cellular Response to Stimulus | ||||
---|---|---|---|---|
Network Measurements | LRD3 | LRD4 | LRD1 | LRD2 |
Spectral gap | 0.3347 | 6.172 | 2.013 | 0.099 |
Density | 0.0489 | 0.0711 | 0.022 | 0.0037 |
Diameter | 1 | 1 | 1 | 1 |
Conn. Comps. | 3 | 2 | 3 | 28 |
Cellular Response to Stress | ||||
Spectral gap | 0.7923 | 4.69 | 0.99 | 0.099 |
Density | 0.027 | 0.087 | 0.102 | 0.0104 |
Diameter | 2 | 1 | 1 | 1 |
Conn. Comps. | 9 | 1 | 5 | 17 |
DNA Metabolic Process | ||||
Spectral gap | 0.858 | 1.202 | 0.99 | 0.4112 |
Density | 0.5714 | 0.038 | 0.166 | 0.0059 |
Diameter | 1 | 1 | 1 | 2 |
Conn. Comps | 6 | 2 | 3 | 69 |
Cellular Response to DNA Damage Stimulus | ||||
Spectral gap | 0.068 | 5.74 | 0.99 | 0.1399 |
Density | 0.055 | 0.058 | 0.166 | 0.0074 |
Diameter | 1 | 1 | 1 | 2 |
Conn. Comps. | 7 | 1 | 3 | 55 |
Network Measurements | DNA Metabolic Process | Nucleic Acid Response Process | ||
---|---|---|---|---|
HZE | γR | HZE | γR | |
Density | 0.1782 | 0.2040 | 0.2465 | 0.2211 |
Spectral gap | 7.5153 | 8.9726 | 12.2554 | 10.4919 |
Diameter | 2 | 4 | 2 | 5 |
Subnetwork with Hub-Gene | Jaccard Similarity Index between HZE and γR Subnetworks | |
DNA Metabolic Process | Nucleic Acid Response Process | |
AT1G09815 | 0.5789 | 0.5789 |
AT2G31320 | 0.6176 | 0.6176 |
AT4G21070 | 0.7619 | - |
AT1G13330 | 0.4814 | 0.4285 |
AT4G29170 | 0.4444 | 0.4444 |
AT2G46610 | - | 0.6250 |
Subnetwork with hub-gene | Jaccard similarity index between LRD3 and LRD4 subnetworks | |
DNA metabolic process and Response to DNA damage to stimulus | DNA metabolic process & Response to DNA damage to stimulus | |
AT3G27060 | 1.0 | 0.1224 |
Arabidopsis Gene Identifier | Gene Coding Protein Description |
---|---|
AT3G13380 | Protein binding, protein serine kinase activity |
AT3G61630 | Cotyledon development, embryo development ending in seed dormancy, leaf development, regulation of transcription, DNA-templated |
AT5G61600 | Cell division, defense response to fungus, phloem or xylem histogenesis, positive regulation of transcription, DNA-templated |
AT3G27060 | Directly involved in synthesis of deoxyribonucleotides, DNA repair, DNA replication, multicellular organism development, programmed cell death, regulation of cell cycle |
AT3G51920 | Response to salt stress and water deprivation, calcium ion binding. |
AT1G70940 | Positive gravitropism, regulation of root meristem growth, response to light stimulus, root development, root hair elongation, root hair initiation |
AT5G48720 | DNA repair, female meiotic nuclear division, pollen development, response to X-ray |
AT2G31320 | DNA ADP-ribosylation, DNA repair, double-strand break repair, protein ADP-ribosylation, protein poly-ADP-ribosylation, response to abscisic acid, response to oxidative stress |
AT4G21070 | DNA recombination, DNA repair, cellular response to gamma radiation, double-strand break repair via homologous recombination, negative regulation of fatty acid biosynthetic process |
AT2G46610 | mRNA splicing, via spliceosome, RNA binding, protein binding |
AT3G21280 | Protein deubiquitination, ubiquitin-dependent protein catabolic process |
AT1G07500 | Cellular response to DNA damage stimulus, negative regulation of mitotic nuclear division, regulation of DNA endoreduplication |
AT5G66140 | Proteasomal ubiquitin-independent protein catabolic process |
AT1G27940 | ATPase-coupled transmembrane transporter activity and nucleotide binding |
AT3G60420 | Phosphoglycerate mutase family protein |
AT4G28950 | Meiotic DNA repair, pollen development, and responds to X-ray |
AT1G23000 | Heavy metal transport/detoxification superfamily protein involved in metal ion transport |
AT1G15580 | Regulation of transcription, DNA-templated, response to auxin |
Arabidopsis Gene Identifier | Gene Coding Protein Description |
---|---|
AT1G01470 | Induced in response to wounding and light stress. Might be involved in protection against desiccation. |
AT1G06390 | This gene is involved in response to osmotic stress. This protein can interact with the BZR1 protein involved in brassinosteroid-mediated signaling in a Y2H assay and promotes BZR1 phosphorylation in protoplasts. |
AT1G05850 | Essential for tolerance to heat, salt and drought stresses. Also involved in root hair development, cell expansion and response to cytokinin. |
AT1G05680 | This enzyme can also transfer glycosyl groups to several compounds related to the explosive TNT when this synthetic compound is taken up from the environment. |
AT1G05620 | Transcript levels for this gene are elevated in older leaves suggesting that it may play a role in purine catabolism during senescence. |
AT3G22370 | Plays a role in shoot acclimation to low temperature. Also is capable of ameliorating reactive oxygen species production when the cytochrome pathway is inhibited. |
AT5G43680 | The protein is localized to the inner mitochondrial membrane that is nuclear-encoded and is essential for plant growth and development. |
AT2G19620 | Plays a role in dehydration stress response. |
AT4G34410 | Direct participation in auxin biosynthesis leading to the plant’s ability to tolerate salt stress. |
AT2G19620 | Plays a role in dehydration stress response. |
AT4G31480 | Required for plant growth, salt tolerance, and maintenance of the structure of the Golgi apparatus. |
AT1G72490 | It is expressed in roots and involved in leaf root architecture, specifically the orientation of lateral root angles |
AT5G61020 | Involved in cell proliferation during plant organogenesis. |
AT5G45420 | Plays a role in root hair elongation. |
Important role in controlling root skewing and maintaining the microtubule network. | |
AT4G35100 | Salt-stress-inducible Major Intrinsic Protein (MIP) |
AT1G13900 | Encodes a dual-localized acid phosphatase (mitochondria and chloroplast) that modulates carbon metabolism. |
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Manian, V.; Orozco-Sandoval, J.; Diaz-Martinez, V. Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight. Genes 2021, 12, 938. https://doi.org/10.3390/genes12060938
Manian V, Orozco-Sandoval J, Diaz-Martinez V. Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight. Genes. 2021; 12(6):938. https://doi.org/10.3390/genes12060938
Chicago/Turabian StyleManian, Vidya, Jairo Orozco-Sandoval, and Victor Diaz-Martinez. 2021. "Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight" Genes 12, no. 6: 938. https://doi.org/10.3390/genes12060938
APA StyleManian, V., Orozco-Sandoval, J., & Diaz-Martinez, V. (2021). Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight. Genes, 12(6), 938. https://doi.org/10.3390/genes12060938