Abstract
Regulatory network is often characterized by complex interactions between transcription factors (TFs) and target genes. The synergistic regulations among multiple TFs may co-induce/co-suppress the expressions of the similar target genes. Such information is important for understanding stress response signaling pathways in plants. In this chapter, we present a computational tool, CoReg, for mining co-regulatory gene modules from network topology. The analysis results can be used to interpret co-regulation effects in regulatory networks generated by high-through TF–DNA interaction screenings such as yeast-one-hybrid, ChIP-seq, and DAP-seq.
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References
Reece-Hoyes JS, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S et al (2011) Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network map**. Nat Methods 8:1059–1064
Bulyk ML (2006) Protein binding microarrays for the characterization of DNA-protein interactions. Adv Biochem Eng Biotechnol 104:65–68
Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide map** of in vivo protein-DNA interactions. Science 316:1497–1502
O’Malley RC, Huang SSC, Song L, Lewsey MG, Bartlett A, Nery JR et al (2016) Cistrome and epicistrome features shape the regulatory DNA landscape. Cell 165:1280–1292
Liu W, Stewart CN (2016) Plant synthetic promoters and transcription factors. Curr Opin Biotechnol 27:36–44
Wu WS, Lai FJ (2015) Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out. BMC Syst Biol 9(Suppl 6): S2
Song Q, Grene R, Heath LS, Li S (2017) Identification of regulatory modules in genome scale transcription regulatory networks. BMC Syst Biol 11:140
Taylor-Teeples M, Lin L, De Lucas M, Turco G, Toal TW, Gaudinier A et al (2015) An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517: 571–575
Acknowledgments
We thank Virginia Agricultural Experiment Station (Blacksburg), USADA National Institute of Food and Agriculture, US Department of Agriculture (Washington, DC) for supporting the development of CoReg.
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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
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Song, Q., Li, S. (2023). Identification of Plant Co-regulatory Modules Using CoReg. In: Song, Q., Tao, Z. (eds) Transcription Factor Regulatory Networks. Methods in Molecular Biology, vol 2594. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2815-7_16
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DOI: https://doi.org/10.1007/978-1-0716-2815-7_16
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Publisher Name: Humana, New York, NY
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