Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Curation of Public Gene Expression Data
2.2. Gene Expression Quantification
2.3. Calculation of HN-Ratio and HN-Score
2.4. Functional Annotation of Transcripts
2.5. Gene Set Enrichment Analysis
2.6. Protein–Protein Interaction Analysis
3. Results
3.1. Curation of RNA-Seq Data for Meta-Analysis
3.2. Characteristics of Upregulated Transcripts under Hypoxia
3.3. Characteristics of Downregulated Transcripts under Hypoxia
3.4. Identification of Commonly Upregulated or Downregulated Genes in Arabidopsis and Rice
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Up or Down | HN-Score (S) | No. of Transcripts |
---|---|---|---|
Arabidopsis | upregulated | 11 ≤ S ≤ 26 | 561 |
Arabidopsis | downregulated | −21 ≤ S ≤ −9 | 493 |
Rice | upregulated | 11 ≤ S ≤ 21 | 606 (477) 1 |
Rice | downregulated | −22 ≤ S ≤ −10 | 570 (489) 1 |
Gene ID | Gene Name | Meta-Analysis 1 |
---|---|---|
AT1G72360 | HRE1 | Up |
AT2G47520 | HRE2 | Up |
AT1G53910 | RAP2.12 | – |
AT3G14230 | RAP2.2 | – |
AT3G16770 | RAP2.3 | – |
AT3G02550 | LBD41 | Up |
AT5G15120 | PCO1 | Up |
AT5G39890 | PCO2 | Up |
AT1G77120 | ADH1 | Up |
AT4G33070 | PDC1 | Up |
Gene ID | Gene Name | In GO:0071456 1 | Gene ID | Gene Name | In GO:0071456 1 |
---|---|---|---|---|---|
AT1G80840 | WRKY40 | – | AT2G46400 | WRKY46 | Yes |
AT1G77120 | ADH1 | Yes | AT3G11820 | SYP121 | – |
AT5G24530 | DMR6 | Yes | AT5G39890 | PCO2 | Yes |
AT4G20860 | FAD-OXR | Yes | AT3G11930 | – | – |
AT3G22060 | CRRSP38 | – | AT2G23810 | TET8 | – |
AT1G18390 | – | – | AT4G10265 | – | Yes |
AT1G15670 | – | – | AT5G06320 | NHL3 | Yes |
AT1G72210 | BHLH96 | – | AT1G43800 | S-ACP-DES6 | Yes |
AT3G61060 | AtPP2-A13 | – | AT2G38470 | WRKY33 | – |
AT4G33050 | EDA39 | – | AT5G50200 | NRT3.1 | – |
AT5G47060 | – | Yes | AT3G29970 | – | – |
AT4G10270 | – | – | AT3G02550 | LBD41 | Yes |
AT1G72360 | HRE1 | Yes | AT2G30490 | CYP73A5 | – |
AT4G23810 | WRKY53 | – | AT4G27450 | – | Yes |
AT2G47520 | ERF071 | Yes | AT1G68840 | RAV2 | Yes |
AT1G14870 | PCR2 | – | AT2G19590 | ACO1 | – |
AT5G41080 | GDPD2 | Yes | AT2G40000 | HSPRO2 | Yes |
AT5G48540 | CRRSP55 | – | AT2G36690 | ||
AT1G25560 | TEM1 | Yes | AT5G06570 | – | – |
AT5G25930 | – | – | AT5G64120 | PER71 | – |
Gene ID | Gene Name | Gene ID | Gene Name | Gene ID | Gene Name |
---|---|---|---|---|---|
AT4G35100 | PIP2;7 | AT2G39890 | PROT1 | AT5G50740 | – |
AT3G45780 | PHOT1 | AT2G29630 | THIC | AT5G57180 | CIA2 |
AT2G38760 | ANN3 | AT1G28570 | – | AT4G23400 | PIP1;5 |
AT4G18570 | – | AT1G16880 | ACR11 | AT3G55760 | – |
AT4G19170 | CCD4 | AT5G42510 | DIR1 | AT1G62180 | APR2 |
AT1G20020 | LFNR2 | AT3G18000 | NMT1 | ||
AT5G11420 | – | AT5G05980 | FPGS1 |
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Tamura, K.; Bono, H. Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia. Life 2022, 12, 1079. https://doi.org/10.3390/life12071079
Tamura K, Bono H. Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia. Life. 2022; 12(7):1079. https://doi.org/10.3390/life12071079
Chicago/Turabian StyleTamura, Keita, and Hidemasa Bono. 2022. "Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia" Life 12, no. 7: 1079. https://doi.org/10.3390/life12071079