LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Wang, Mingyi ^a   Verdier, Jerome ^a   Benedito, Vagner A ^b   Tang, Yuhong ^a   Murray, Jeremy D ^c   Ge, Yinbing ^a   Becker, Jörg D ^d   Carvalho, Helena ^e   Rogers, Christian ^c   Udvardi, Michael ^a   He, Ji ^a,f  

^a PLANT BIOLOGY DIVISION   (United States)

^b WEST VIRGINIA UNIVERSITY   (United States)

^c JOHN INNES CENTRE   (United Kingdom)

^d INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^e UNIVERSITY OF PORTO   (Portugal)

^f SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BARREL MEDIC; BAYES THEOREM; COMPARATIVE STUDY; COMPUTER NETWORK; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTEXT LIKELIHOOD OF RELATEDNESS; FUNCTIONAL GENOMICS; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENIE3 ALGORITHM; GRAPHICAL GAUSSIAN MODEL; INTERNET; LEARNING ALGORITHM; LEGUME; LOTUS JAPONICUS; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; PLANT GENE; PROTEIN DATABASE; SOYBEAN; STATISTICAL ANALYSIS; STATISTICAL MODEL; TIGRESS ALGORITHM; TRANSCRIPTOMICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; INTERNET; LOTUS; MEDICAGO; SOFTWARE; SOYBEANS;

GLYCINE MAX; LOTUS CORNICULATUS VAR. JAPONICUS; MEDICAGO TRUNCATULA;

EID: 84879768023     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067434     Document Type: Article

References (42)

1. Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, et al. (2008) A gene expression atlas of the model legume Medicago truncatula. Plant J 55: 504-513.
2. He J, Benedito VA, Wang M, Murray JD, Zhao PX, et al. (2009) The Medicago truncatula gene expression atlas web server. BMC Bioinformatics 10: 441.
3. Verdier J, Torres-Jerez I, Wang M, Andriankaja A, Allen SN, et al. (2013) Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation. Plant J 74: 351-362.
4. Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K, (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 37: D987-991.
5. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, et al. (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38Suppl: W214-220.
6. Lee TH, Kim YK, Pham TT, Song SI, Kim JK, et al. (2009) RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol 151: 16-33.
7. Ogata Y, Suzuki H, Sakurai N, Shibata D, (2010) CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26: 1267-1268.
8. 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: 149-156.
9. Marbach D, Costello JC, Kuffner R, Vega NM, Prill RJ, et al. (2012) Wisdom of crowds for robust gene network inference. Nat Methods 9: 796-804.
10. Haibe-Kains B, Olsen C, Djebbari A, Bontempi G, Correll M, et al. (2011) Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Res 40: D866-875.
11. Stuart JM, Segal E, Koller D, Kim SK, (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255.
12. Schafer J, Strimmer K, (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21: 754-764.
13. Xiao Y, (2009) A tutorial on analysis and simulation of boolean gene regulatory network models. Curr Genomics 10: 511-525.
14. Kim H, Lee JK, Park T, (2007) Boolean networks using the chi-square test for inferring large-scale gene regulatory networks. BMC Bioinformatics 8: 37.
15. Chen T, He HL, Church GM (1999) Modeling gene expression with differential equations. Pac Symp Biocomput: 29-40.
16. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, et al. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5: e8.
17. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, et al. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7Suppl 1: S7.
18. Friedman N, Linial M, Nachman I, Pe'er D, (2000) Using bayesian networks to analyze expression data. Journal of computational biology 7: 601-620.
19. Watanabe Y, Seno S, Takenaka Y, Matsuda H, (2012) An estimation method for inference of gene regulatory net-work using Bayesian network with uniting of partial problems. BMC Genomics 13Suppl 1: S12.
20. Haury A-CM, Fantine; Vera-Licona, Paola; Vert, Jean-Philippe (2012) TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. Preprint at .
21. Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P (2010) Inferring regulatory networks from expression data using tree-based methods. PLoS One 5.
22. Kuffner R, Petri T, Tavakkolkhah P, Windhager L, Zimmer R, (2012) Inferring gene regulatory networks by ANOVA. Bioinformatics 28: 1376-1382.
23. De Smet R, Marchal K, (2010) Advantages and limitations of current network inference methods. Nat Rev Microbiol 8: 717-729.
24. Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, et al. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A 107: 6286-6291.
25. Wang M, Augusto Benedito V, Xuechun Zhao P, Udvardi M, (2010) Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm. Mol Biosyst 6: 988-998.
26. Haury AC, Mordelet F, Vera-Licona P, Vert JP, (2012) TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. BMC Syst Biol 6: 145.
27. Stolovitzky G, Monroe D, Califano A, (2007) Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Ann N Y Acad Sci 1115: 1-22.
28. Colombo DM, Marloes H. (2012) A modification of the PC algorithm yielding order-independent skeletons. Preprint at .
29. Opitz D, Maclin R, (1999) Popular ensemble methods: An empirical study. Journal of Artificial Intelligence Research 11: 12.
30. Marder E, Taylor AL, (2011) Multiple models to capture the variability in biological neurons and networks. Nat Neurosci 14: 133-138.
31. Prinz AA, Bucher D, Marder E, (2004) Similar network activity from disparate circuit parameters. Nat Neurosci 7: 1345-1352.
32. de Borda JC (1781) Memoire sur les elections au scrutin, historie de l'academie royale des sciences.
33. Moreno-Hagelsieb G, Latimer K, (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24: 319-324.
34. Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, et al. (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144: 329-338.
35. Goffard N, Weiller G, (2007) GeneBins: a database for classifying gene expression data, with application to plant genome arrays. BMC Bioinformatics 8: 87.
36. Goffard N, Weiller G, (2006) Extending MapMan: application to legume genome arrays. Bioinformatics 22: 2958-2959.
37. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, et al. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347-2348.
38. Monke G, Seifert M, Keilwagen J, Mohr M, Grosse I, et al. (2012) Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res 40: 8240-8254.
39. Parcy F, Valon C, Kohara A, Misera S, Giraudat J, (1997) The ABSCISIC ACID-INSENSITIVE3, FUSCA3, and LEAFY COTYLEDON1 loci act in concert to control multiple aspects of Arabidopsis seed development. Plant Cell 9: 1265-1277.
40. Teng S, Rognoni S, Bentsink L, Smeekens S, (2008) The Arabidopsis GSQ5/DOG1 Cvi allele is induced by the ABA-mediated sugar signalling pathway, and enhances sugar sensitivity by stimulating ABI4 expression. Plant J 55: 372-381.
41. Brown G, Wyatt J, Harris R, Yao X, (2005) Diversity creation methods: a survey and categorisation. Information Fusion 6: 5-20.
42. Zhou Z-H, Li N (2010) Multi-information ensemble diversity. Multiple Classifier Systems: Springer. 134-144.