Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters
Abstract
:1. Introduction
2. Materials and Methods
2.2. Arabidopsis interactome network and clustering analysis
2.3. Promoter analysis
3. Results
3.1. Expression correlation and gene ontology (GO) analyses
3.2. Interactome analysis
3.3. Promoter analysis
4. Discussion
4.1. SPL genes may play a key role in the stress response
4.2. A complex control network linking SPL genes and other transcription families
4.3. SPL genes and integral membrane proteins
4.4. SPL genes may regulate themselves
4.5. SPL genes have varied functions
5. Conclusion
Appendix: Supplementary Material
Acknowledgments
References
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AGI ID | Annotation | AGI ID | Annotation |
---|---|---|---|
AT5G20960 | ALDEHYDE OXIDASE 1 | AT3G18850 | LPAT5__LPAT5 |
AT1G52030 | MYROSINASE-BINDING PROTEIN 2 | AT4G00870 | basic helix-loop-helix (bHLH) family protein |
AT2G26650 | ARABIDOPSIS K TRANSPORTER 1 | AT5G37020 | ARF8 |
AT3G55110 | ABC transporter family protein | AT3G09260 | phosphate starvation-response 3.1 oxidoreductase, 2OG-Fe(II) oxygenase family |
AT4G15440 | HYDROPEROXIDE LYASE 1 | AT5G20400 | protein |
AT3G06160 | transcriptional factor B3 family protein | AT4G19430 | unknown protein |
AT5G44380 | FAD-binding domain-containing protein | AT5G17820 | peroxidase 57 (PER57) (P57) (PRXR10) |
AT5G60910 | FUL | AT3G06220 | DNA binding / transcription factor |
AT2G42200 | SPL9 | AT5G45960 | GDSL-motif lipase/hydrolase family protein |
AT2G45430 | DNA-binding protein-related | AT4G21650 | subtilase family protein UCC2__UCC2 (UCLACYANIN 2); copper |
AT3G04570 | DNA-binding protein-related | AT2G44790 | ion binding |
AT4G32650 | ARABIDOPSIS THALIANA K+ RECTIFYING CHANNEL 1 | AT3G28500 | 60S acidic ribosomal protein P2 (RPP2C) |
AT3G14680 | CYP72A14 | AT4G12550 | Auxin-Induced in Root cultures 1 |
AT1G20900 | ESCAROLA | AT4G20860 | FAD-binding domain-containing protein |
AT1G60680 | ARF-GAP DOMAIN 2 | AT4G28680 | tyrosine decarboxylase, putative |
AT3G53130 | LUTEIN DEFICIENT 1 | AT5G63600 | flavonol synthase, putative |
AT3G51895 | SULFATE TRANSPORTER 1 | AT2G01760 | ARABIDOPSIS RESPONSE REGULATOR 14 |
AT2G47000 | P-GLYCOPROTEIN 4 | AT5G59000 | zinc finger (C3HC4-type RING finger) family protein |
AT4G39675 | unknown protein | AT5G03700 | PAN domain-containing protein |
AT5G24420 | glucosamine/galactosamine-6-phosphate isomerase-related | AT2G21045 | similar to unknown protein |
AT3G24240 | leucine-rich repeat transmembrane protein kinase, putative | AT5G50760 | auxin-responsive family protein |
AT1G72260 | toxin receptor binding | AT3G15950 | (TSA1-LIKE); unknown protein |
AT3G15270 | SPL5 | AT1G17860 | trypsin and protease inhibitor family protein |
AT2G33810 | SPL3 | AT2G20870 | cell wall protein precursor, putative |
AT1G53160 | SPL4 | AT5G20550 | oxidoreductase |
AT5G05880 | UDP-glucosyl transferase family protein | AT1G05000 | tyrosine specific protein phosphatase family protein |
AT1G24070 | Cellulose synthase-like A10 | AT3G43600 | AAO2 |
AT3G20370 | MATH domain-containing protein | AT4G22200 | Arabidopsis K+ transporter 2 |
AT5G26280 | MATH domain-containing protein | AT3G21720 | isocitrate lyase, putative |
AT1G51460 | ABC transporter family protein | AT1G52410 | TSK-ASSOCIATING PROTEIN 1 |
AT3G16460 | jacalin lectin family protein | AT4G19880 | similar to unknown protein |
AT3G53480 | PLEIOTROPIC DRUG RESISTANCE 9 | AT2G18980 | peroxidase, putative |
AT5G44620 | CYP706A3 | AT1G18980 | germin-like protein, putative |
AT5G01040 | laccase 8 | AT4G13180 | short-chain dehydrogenase |
AT5G65210 | TGA1 | AT5G63590 | Flavonol synthase |
AT1G52400 | BGL1 | AT3G03090 | ATVGT1__sugar transporter family protein |
AT5G14370 | similar to CIL | AT3G25820 | TERPENE SYNTHASE-LIKE SEQUENCE-1,8-CINEOLE |
AT1G66270 | beta-glucosidase | AT4G15210 | BETA-AMYLASE |
AT5G02030 | HB-6_RPL_LSN_BLH9_BLR_PNY_RPL_VAN__LSN | AT2G42350 | zinc finger family protein |
AT4G13660 | pinoresinol-lariciresinol reductase, putative | AT3G50300 | transferase family protein |
AT4G15390 | transferase family protein | AT3G03520 | phosphoesterase family protein |
AT5G64100 | peroxidase, putative | AT1G15210 | PLEIOTROPIC DRUG RESISTANCE 7 |
AT1G78000 | SULFATE TRANSPORTER 1;2 | AT3G16420 | PYK10-BINDING PROTEIN 1 |
AT1G29280 | WRKY DNA-binding protein 65 | AT3G13790 | ARABIDOPSIS THALIANA CELL WALL INVERTASE 1 |
AT2G39330 | jacalin lectin family protein | AT3G62270 | anion exchange family protein |
AT1G09740 | ethylene-responsive protein, putative | AT4G25820 | XYLOGLUCAN ENDOTRANSGLYCOSYLASE 9 |
AT1G22440 | alcohol dehydrogenase, putative | AT1G27370 | SPL10 |
AT5G26260 | MATH domain-containing protein | AT5G66985 | unknown protein |
AT2G25980 | jacalin lectin family protein | AT3G26770 | short-chain dehydrogenase |
AT1G31550 | carboxylic ester hydrolase/lipase | AT3G11000 | similar to kelch repeat-containing protein |
AT1G19530 | unknown protein | AT3G14940 | PHOSPHOENOLPYRUVATE CARBOXYLASE 3 |
AT1G74430 | AtMYB95 | AT1G44760 | universal stress protein (USP) family protein |
AT2G04090 | MATE efflux family protein | AT1G14210 | ribonuclease T2 family protein |
AT5G35580 | kinase | AT1G27360 | SPL11 |
AT3G53310 | transcriptional factor B3 family protein | AT1G69170 | SPL6 |
AT5G50570 | SPL13 | AT3G57920 | SPL15 |
© 2009 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/3.0/). This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/3.0/).
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Wang, Y.; Hu, Z.; Yang, Y.; Chen, X.; Chen, G. Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters. Int. J. Mol. Sci. 2009, 10, 116-132. https://doi.org/10.3390/ijms10010116
Wang Y, Hu Z, Yang Y, Chen X, Chen G. Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters. International Journal of Molecular Sciences. 2009; 10(1):116-132. https://doi.org/10.3390/ijms10010116
Chicago/Turabian StyleWang, Yi, Zongli Hu, Yuxin Yang, Xuqing Chen, and Guoping Chen. 2009. "Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters" International Journal of Molecular Sciences 10, no. 1: 116-132. https://doi.org/10.3390/ijms10010116