AtGGM2014, an Arabidopsis gene co-expression network for functional studies

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• 作者：ShiSong Ma (1)
  Hans J. Bohnert (2)
  Savithramma P. Dinesh-Kumar (1)
  
  1. Department of Plant Biology and the Genome Center ; College of Biological Sciences ; University of California ; Davis ; CA ; 95616 ; USA
  2. Departments of Plant Biology and of Crop Sciences ; University of Illinois at Urbana-Champaign ; Urbana ; IL ; 61801 ; USA
  
• 关键词：Arabidopsis ; gene co ; expression network ; graphical Gaussian model ; plant development ; stress response ; hormone response
• 刊名：Science China Life Sciences
• 出版年：2015
• 出版时间：March 2015
• 年：2015
• 卷：58
• 期：3
• 页码：276-286
• 全文大小：2,013 KB
• 参考文献：1. Mentzen, WI, Wurtele, ES (2008) Regulon organization of Arabidopsis. BMC Plant Biol 8: pp. 99 471-2229-8-99" target="_blank" title="It opens in new window">CrossRef
  2. Mao, L, Hemert, JL, Dash, S, Dickerson, JA (2009) Arabidopsis gene coexpression network and its functional modules. BMC Bioinformatics 10: pp. 346 471-2105-10-346" target="_blank" title="It opens in new window">CrossRef
  3. Zhang, W, Morris, QD, Chang, R, Shai, O, Bakowski, MA, Mitsakakis, N, Mohammad, N, Robinson, MD, Zirngibl, R, Somogyi, E, Laurin, N, Eftekharpour, E, Sat, E, Grigull, J, Pan, Q, Peng, WT, Krogan, N, Greenblatt, J, Fehlings, M, Kooy, D, Aubin, J, Bruneau, BG, Rossant, J, Blencowe, BJ, Frey, BJ, Hughes, TR (2004) The functional landscape of mouse gene expression. J Biol 3: pp. 21 CrossRef
  4. Ghazalpour, A, Doss, S, Zhang, B, Wang, S, Plaisier, C, Castellanos, R, Brozell, A, Schadt, EE, Drake, TA, Lusis, AJ, Horvath, S (2006) Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet 2: pp. e130 CrossRef
  5. Song, L, Langfelder, P, Horvath, S (2012) Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics 13: pp. 328 471-2105-13-328" target="_blank" title="It opens in new window">CrossRef
  6. Zhang, B, Horvath, S (2005) A general framework for weighted gene coexpression network analysis. Stat Appl Genet Mol Biol 4: pp. Article17
  7. Friedman, N, Linial, M, Nachman, I, Pe鈥檈r, D (2000) Using Bayesian net works to analyze expression data. J Comput Biol 7: pp. 601-620 CrossRef
  8. Ma, S, Gong, Q, Bohnert, HJ (2007) An Arabidopsis gene network based on the graphical Gaussian model. Genome Res 17: pp. 1614-1625 CrossRef
  9. Schafer, J, Strimmer, K (2005) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat Appl Genet Mol Biol 4: pp. Article32
  10. Wille, A, Zimmermann, P, Vranova, E, Furholz, A, Laule, O, Bleuler, S, Hennig, L, Prelic, A, Rohr, P, Thiele, L, Zitzler, E, Gruissem, W, Buhlmann, P (2004) Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana. Genome Biol 5: pp. R92 4-5-11-r92" target="_blank" title="It opens in new window">CrossRef
  11. Rustici, G, Kolesnikov, N, Brandizi, M, Burdett, T, Dylag, M, Emam, I, Farne, A, Hastings, E, Ison, J, Keays, M, Kurbatova, N, Malone, J, Mani, R, Mupo, A, Pedro Pereira, R, Pilicheva, E, Rung, J, Sharma, A, Tang, YA, Ternent, T, Tikhonov, A, Welter, D, Williams, E, Brazma, A, Parkinson, H, Sarkans, U (2013) ArrayExpress update-trends in database growth and links to data analysis tools. Nucleic Acids Res 41: pp. D987-990 4" target="_blank" title="It opens in new window">CrossRef
  12. Kauffmann, A, Gentleman, R, Huber, W (2009) arrayQualityMetrics鈥攁 bioconductor package for quality assessment of microarray data. Bioinformatics 25: pp. 415-416 47" target="_blank" title="It opens in new window">CrossRef
  13. Wu, ZJ, Irizarry, RA, Gentleman, R, Martinez-Murillo, F, Spencer, F (2004) A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 99: pp. 909-917 4504000000683" target="_blank" title="It opens in new window">CrossRef
  14. Lamesch, P, Berardini, TZ, Li, D, Swarbreck, D, Wilks, C, Sasidharan, R, Muller, R, Dreher, K, Alexander, DL, Garcia-Hernandez, M, Karthikeyan, AS, Lee, CH, Nelson, WD, Ploetz, L, Singh, S, Wensel, A, Huala, E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40: pp. D1202-1210 CrossRef
  15. Bolstad, BM, Irizarry, RA, Astrand, M, Speed, TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: pp. 185-193 CrossRef
  16. Theocharidis, A, Dongen, S, Enright, AJ, Freeman, TC (2009) Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc 4: pp. 1535-1550 CrossRef
  17. Gansner, ER, North, SC (2000) An open graph visualization system and its applications to software engineering. Softw Pract Exp 30: pp. 1203-1233 4X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N" target="_blank" title="It opens in new window">CrossRef
  18. Enright, AJ, Dongen, S, Ouzounis, CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: pp. 1575-1584 CrossRef
  19. Dongen, S (2000) Graph clustering by flow simulation. Dessertation for Doctoral Degree. Utrecht University, Utrecht
  20. Falcon, S, Gentleman, R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23: pp. 257-258 CrossRef
  21. Goda, H, Sasaki, E, Akiyama, K, Maruyama-Nakashita, A, Nakabayashi, K, Li, W, Ogawa, M, Yamauchi, Y, Preston, J, Aoki, K, Kiba, T, Takatsuto, S, Fujioka, S, Asami, T, Nakano, T, Kato, H, Mizuno, T, Sakakibara, H, Yamaguchi, S, Nambara, E, Kamiya, Y, Takahashi, H, Hirai, MY, Sakurai, T, Shinozaki, K, Saito, K, Yoshida, S, Shimada, Y (2008) The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J 55: pp. 526-542 CrossRef
  22. Kilian, J, Whitehead, D, Horak, J, Wanke, D, Weinl, S, Batistic, O, D鈥橝ngelo, C, Bornberg-Bauer, E, Kudla, J, Harter, K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50: pp. 347-363 CrossRef
  23. Schmid, M, Davison, TS, Henz, SR, Pape, UJ, Demar, M, Vingron, M, Scholkopf, B, Weigel, D, Lohmann, JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: pp. 501-506 43" target="_blank" title="It opens in new window">CrossRef
  24. Wang, D, Weaver, ND, Kesarwani, M, Dong, X (2005) Induction of protein secretory pathway is required for systemic acquired resistance. Science 308: pp. 1036-1040 CrossRef
  25. Benkova, E, Michniewicz, M, Sauer, M, Teichmann, T, Seifertova, D, Jurgens, G, Friml, J (2003) Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell 115: pp. 591-602 4(03)00924-3" target="_blank" title="It opens in new window">CrossRef
  26. McConnell, JR, Emery, J, Eshed, Y, Bao, N, Bowman, J, Barton, MK (2001) Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature 411: pp. 709-713 CrossRef
  27. Long, JA, Ohno, C, Smith, ZR, Meyerowitz, EM (2006) TOPLESS regulates apical embryonic fate in Arabidopsis. Science 312: pp. 1520-1523 41" target="_blank" title="It opens in new window">CrossRef
  28. Cheng, Y, Dai, X, Zhao, Y (2007) Auxin synthesized by the YUCCA flavin monooxygenases is essential for embryogenesis and leaf formation in Arabidopsis. Plant Cell 19: pp. 2430-2439 CrossRef
  29. Hou, H, Erickson, J, Meservy, J, Schultz, EA (2010) FORKED1 encodes a PH domain protein that is required for PIN1 localization in developing leaf veins. Plant J 63: pp. 960-973 4291.x" target="_blank" title="It opens in new window">CrossRef
  30. O鈥橫aoileidigh, DS, Graciet, E, Wellmer, F (2014) Gene networks controlling Arabidopsis thaliana flower development. New Phytol 201: pp. 16-30 444" target="_blank" title="It opens in new window">CrossRef
  31. Bowman, JL, Smyth, DR, Meyerowitz, EM (2012) The ABC model of flower development: then and now. Development 139: pp. 4095-4098 42/dev.083972" target="_blank" title="It opens in new window">CrossRef
  32. Wagner, D, Meyerowitz, EM (2011) Switching on Flowers: transient LEAFY induction reveals novel aspects of the regulation of reproductive development in Arabidopsis. Front Plant Sci 2: pp. 60 CrossRef
  33. Crawford, BC, Ditta, G, Yanofsky, MF (2007) The NTT gene is required for transmitting-tract development in carpels of Arabidopsis thaliana. Curr Biol 17: pp. 1101-1108 CrossRef
  34. Baudry, A, Heim, MA, Dubreucq, B, Caboche, M, Weisshaar, B, Lepiniec, L (2004) TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J 39: pp. 366-380 4.02138.x" target="_blank" title="It opens in new window">CrossRef
  35. Reeves, PH, Ellis, CM, Ploense, SE, Wu, MF, Yadav, V, Tholl, D, Chetelat, A, Haupt, I, Kennerley, BJ, Hodgens, C, Farmer, EE, Nagpal, P, Reed, JW (2012) A regulatory network for coordinated flower maturation. PLoS Genet 8: pp. e1002506 CrossRef
  36. Matias-Hernandez, L, Battaglia, R, Galbiati, F, Rubes, M, Eichenberger, C, Grossniklaus, U, Kater, MM, Colombo, L (2010) VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis. Plant Cell 22: pp. 1702-1715 CrossRef
  37. Cucinotta, M, Colombo, L, Roig-Villanova, I (2014) Ovule development, a new model for lateral organ formation. Front Plant Sci 5: pp. 117 4.00117" target="_blank" title="It opens in new window">CrossRef
  38. Guo, H, Ecker, JR (2004) The ethylene signaling pathway: new insights. Curr Opin Plant Biol 7: pp. 40-49 CrossRef
  39. Zhao, Q, Guo, HW (2011) Paradigms and paradox in the ethylene signaling pathway and interaction network. Mol Plant 4: pp. 626-634 42" target="_blank" title="It opens in new window">CrossRef
  40. Hu, Y, Poh, HM, Chua, NH (2006) The Arabidopsis ARGOS-LIKE gene regulates cell expansion during organ growth. Plant J 47: pp. 1-9 CrossRef
  41. Hu, Y, Xie, Q, Chua, NH (2003) The Arabidopsis auxin-inducible gene ARGOS controls lateral organ size. Plant Cell 15: pp. 1951-1961 CrossRef
  42. Millenaar, FF, Cox, MC, Berkel, YE, Welschen, RA, Pierik, R, Voesenek, LA, Peeters, AJ (2005) Ethylene-induced differential growth of petioles in Arabidopsis. Analyzing natural variation, response kinetics, and regulation. Plant Physiol 137: pp. 998-1008 4/pp.104.053967" target="_blank" title="It opens in new window">CrossRef
  43. Hebelstrup, KH, Zanten, M, Mandon, J, Voesenek, LA, Harren, FJ, Cristescu, SM, Moller, IM, Mur, LA (2012) Haemoglobin modulates NO emission and hyponasty under hypoxia-related stress in Arabidopsis thaliana. J Exp Bot 63: pp. 5581-5591 CrossRef
  44. Roine, E, Wei, W, Yuan, J, Nurmiaho-Lassila, EL, Kalkkinen, N, Romantschuk, M, He, SY (1997) Hrp pilus: an hrp-dependent bacterial surface appendage produced by Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 94: pp. 3459-3464 4.7.3459" target="_blank" title="It opens in new window">CrossRef
  45. Liu, Y, Schiff, M, Dinesh-Kumar, SP (2004) Involvement of MEK1 MAPKK, NTF6 MAPK, WRKY/MYB transcription factors, COI1 and CTR1 in N-mediated resistance to tobacco mosaic virus. Plant J 38: pp. 800-809 4.02085.x" target="_blank" title="It opens in new window">CrossRef
  46. Wang, D, Amornsiripanitch, N, Dong, X (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2: pp. e123 CrossRef
  47. Century, KS, Shapiro, AD, Repetti, PP, Dahlbeck, D, Holub, E, Staskawicz, BJ (1997) NDR1, a pathogen-induced component required for Arabidopsis disease resistance. Science 278: pp. 1963-1965 45.1963" target="_blank" title="It opens in new window">CrossRef
  48. Durrant, WE, Dong, X (2004) Systemic acquired resistance. Annu Rev Phytopathol 42: pp. 185-209 46/annurev.phyto.42.040803.140421" target="_blank" title="It opens in new window">CrossRef
  49. Boutilier, K, Offringa, R, Sharma, VK, Kieft, H, Ouellet, T, Zhang, L, Hattori, J, Liu, CM, Lammeren, AA, Miki, BL, Custers, JB, Lookeren Campagne, MM (2002) Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. Plant Cell 14: pp. 1737-1749 41" target="_blank" title="It opens in new window">CrossRef
  50. Millet, YA, Danna, CH, Clay, NK, Songnuan, W, Simon, MD, Werck-Reichhart, D, Ausubel, FM (2010) Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns. Plant Cell 22: pp. 973-990 CrossRef
  51. Zhou, L, Jang, JC, Jones, TL, Sheen, J (1998) Glucose and ethylene signal transduction crosstalk revealed by an Arabidopsis glucose-insensitive mutant. Proc Natl Acad Sci USA 95: pp. 10294-10299 4" target="_blank" title="It opens in new window">CrossRef
  52. Gan, S, Amasino, RM (1997) Making sense of senescence (molecular genetic regulation and manipulation of leaf senescence). Plant Physiol 113: pp. 313-319
  53. Bari, R, Jones, JD (2009) Role of plant hormones in plant defence responses. Plant Mol Biol 69: pp. 473-488 435-0" target="_blank" title="It opens in new window">CrossRef
  54. Ma, S, Shah, S, Bohnert, HJ, Snyder, M, Dinesh-Kumar, SP (2013) Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. PLoS Genet 9: pp. e1003840 40" target="_blank" title="It opens in new window">CrossRef
  55. Popescu, SC, Popescu, GV, Bachan, S, Zhang, Z, Gerstein, M, Snyder, M, Dinesh-Kumar, SP (2009) MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev 23: pp. 80-92 40009" target="_blank" title="It opens in new window">CrossRef
  56. Chang, KN, Zhong, S, Weirauch, MT, Hon, G, Pelizzola, M, Li, H, Huang, SS, Schmitz, RJ, Urich, MA, Kuo, D, Nery, JR, Qiao, H, Yang, A, Jamali, A, Chen, H, Ideker, T, Ren, B, Bar-Joseph, Z, Hughes, TR, Ecker, JR (2013) Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife 2: pp. e00675 4/eLife.00675" target="_blank" title="It opens in new window">CrossRef
  57. Lee, I, Ambaru, B, Thakkar, P, Marcotte, EM, Rhee, SY (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 28: pp. 149-156 CrossRef
  Evidence for network evolution in an Arabidopsis interactome map. Science 333: pp. 601-607 CrossRef
  
• 刊物主题：Life Sciences, general;
• 出版者：Springer Berlin Heidelberg
• ISSN：1869-1889

文摘

Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the ArrayExpress database, we constructed an Arabidopsis gene co-expression network, termed AtGGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. AtGGM2014 offers a constructive tool for plant systems biology studies.