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A Boolean Model of the Cardiac Gene Regulatory Network Determining First and Second Heart Field Identity
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Systematic cardiac gene regulatory networks were previously reported based on spatio-temporal datasets or integration of gene expression and gene regulation.
“Indeed, systematic cardiac GRNs were previously reported, based on either spatio-temporal datasets [44, 45] or integration of layers of gene expression and gene regulation [46].”
From A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease (2021) · cites this paper as [44]
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Thomas, R., & Kaufman, M. (2001) · Chaos: An Interdisciplinary Journal of Nonlinear Science · doi:10.1063/1.1349893 · Cited by 242
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Research works printed but not linked: 49
- [1]Moretti A, Caron L, Nakano A, Lam JT, Bernshausen A, et al (2006) Multipotent embryonic isl1+ progenitor cells lead to cardiac, smooth muscle, and endothelial cell diversification. Cell 127: 1151– 1165. 17123592
- [2]Yang L, Soonpaa MH, Adler ED, Roepke TK, Kattman SJ, et al (2008) Human cardiovascular progenitor cells develop from a KDR+ embryonic-stem-cell-derived population. Nature 453: 524– 528. 18432194
- [3]Buckingham M, Meilhac S, Zaffran S (2005) Building the mammalian heart from two sources of myocardial cells. Nature reviews Genetics 6: 826– 835. 16304598
- [4]Laugwitz KL, Moretti A, Caron L, Nakano A, Chien KR (2008) Islet1 cardiovascular progenitors: a single source for heart lineages? Development 135: 193– 205. 18156162
- [5]Liu P, Wakamiya M, Shea MJ, Albrecht U, Behringer RR, et al (1999) Requirement for Wnt3 in vertebrate axis formation. Nature genetics 22: 361– 365. 10431240
- [6]Kitajima S, Takagi A, Inoue T, Saga Y (2000) MesP1 and MesP2 are essential for the development of cardiac mesoderm. Development 127: 3215– 3226. 10887078
- [7]Liberatore CM, Searcy-Schrick RD, Vincent EB, Yutzey KE (2002) Nkx-2.5 gene induction in mice is mediated by a Smad consensus regulatory region. Developmental biology 244: 243– 256. 11944934
- [8]Lindsley RC, Gill JG, Murphy TL, Langer EM, Cai M, et al (2008) Mesp1 coordinately regulates cardiovascular fate restriction and epithelial-mesenchymal transition in differentiating ESCs. Cell stem cell 3: 55– 68. 18593559 PMC2497439
- [9]Zhang H, Bradley A (1996) Mice deficient for BMP2 are nonviable and have defects in amnion/chorion and cardiac development. Development 122: 2977– 2986. 8898212
- [10]Bondue A, Lapouge G, Paulissen C, Semeraro C, Iacovino M, et al (2008) Mesp1 acts as a master regulator of multipotent cardiovascular progenitor specification. Cell stem cell 3: 69– 84. 18593560
- [11]Cai CL, Liang X, Shi Y, Chu PH, Pfaff SL, et al (2003) Isl1 identifies a cardiac progenitor population that proliferates prior to differentiation and contributes a majority of cells to the heart. Developmental cell 5: 877– 889. 14667410 PMC5578462
- [12]Yamagishi H, Maeda J, Hu T, McAnally J, Conway SJ, et al (2003) Tbx1 is regulated by tissue-specific forkhead proteins through a common Sonic hedgehog-responsive enhancer. Genes & development 17: 269– 281. 12533514 PMC195981
- [13]Kelly RG, Brown NA, Buckingham ME (2001) The arterial pole of the mouse heart forms from Fgf10-expressing cells in pharyngeal mesoderm. Developmental cell 1: 435– 440. 11702954
- [14]Bruneau BG, Logan M, Davis N, Levi T, Tabin CJ, et al (1999) Chamber-specific cardiac expression of Tbx5 and heart defects in Holt-Oram syndrome. Developmental biology 211: 100– 108. 10373308
- [15]de Jong H (2002) Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. Journal of Computational Biology 9: 67– 103. 11911796
- [16]Smith J, Theodoris C, Davidson EH (2007) A Gene Regulatory Network Subcircuit Drives a Dynamic Pattern of Gene Expression. Science 318: 794– 797. 17975065
- [17]MacLean D, Studholme DJ (2010) A Boolean Model of the Pseudomonas syringae hrp Regulon Predicts a Tightly Regulated System. PLoS ONE 5: e9101. 20169167 PMC2821412
- [18]Veliz-Cuba A, Stigler B (2011) Boolean Models Can Explain Bistability in the lac Operon. Journal of Computational Biology 18: 783– 794. 21563979
- [19]Thomas R, Kaufman M (2001) Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior. Chaos: An Interdisciplinary Journal of Nonlinear Science 11: 170– 179. 12779451
- [21]Kauffman SA (1993) The Origins of Order: Self Organization and Selection in Evolution: Oxford University Press.
- [22]Arnold SJ, Stappert J, Bauer A, Kispert A, Herrmann BG, et al (2000) Brachyury is a target gene of the Wnt/beta-catenin signaling pathway. Mechanisms of development 91: 249– 258. 10704849
- [23]Kispert A, Herrmann BG (1994) Immunohistochemical analysis of the Brachyury protein in wild-type and mutant mouse embryos. Dev Biol 161: 179– 193. 8293872
- [24]Wilkinson DG, Bhatt S, Herrmann BG (1990) Expression pattern of the mouse T gene and its role in mesoderm formation. Nature 343: 657– 659. 1689462
- [25]Lin L, Cui L, Zhou W, Dufort D, Zhang X, et al (2007) Beta-catenin directly regulates Islet1 expression in cardiovascular progenitors and is required for multiple aspects of cardiogenesis. PNAS 104: 9313– 9318. 17519333 PMC1890491
- [26]Gessert S, Kühl M (2010) The multiple phases and faces of wnt signaling during cardiac differentiation and development. Circulation research 107: 186– 199. 20651295
- [27]Saga Y, Miyagawa-Tomita S, Takagi A, Kitajima S, Miyazaki J, et al (1999) MesP1 is expressed in the heart precursor cells and required for the formation of a single heart tube. Development (Cambridge, England) 126: 3437– 3447. 10393122
- [28]Saga Y, Kitajima S, Miyagawa-Tomita S (2000) Mesp1 expression is the earliest sign of cardiovascular development. Trends in cardiovascular medicine 10: 345– 352. 11369261
- [29]David R, Brenner C, Stieber J, Schwarz F, Brunner S, et al (2008) MesP1 drives vertebrate cardiovascular differentiation through Dkk-1-mediated blockade of Wnt-signalling. Nature cell biology 10: 338– 345. 18297060
- [30]Kattman SJ, Huber TL, Keller GM (2006) Multipotent flk-1+ cardiovascular progenitor cells give rise to the cardiomyocyte, endothelial, and vascular smooth muscle lineages. Developmental cell 11: 723– 732. 17084363
- [31]Klaus A, Saga Y, Taketo MM, Tzahor E, Birchmeier W (2007) Distinct roles of Wnt/beta-catenin and Bmp signaling during early cardiogenesis. PNAS 104: 18531– 18536. 18000065 PMC2141811
- [32]Phillips MD, Mukhopadhyay M, Poscablo C, Westphal H (2012) Dkk1 and Dkk2 regulate epicardial specification during mouse heart development. International Journal of Cardiology 150: 186– 192. PMC2916964 20439124
- [33]Li S, Brazhnik P, Sobral B, Tyson JJ (2008) A Quantitative Study of the Division Cycle of Caulobacter crescentus Stalked Cells. PLoS Comput Biol 4: e9. 18225942 PMC2217572
- [34]Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, et al (2004) Integrative Analysis of Cell Cycle Control in Budding Yeast. Molecular Biology of the Cell 15: 3841– 3862. 15169868 PMC491841
- [35]Wawra C, Kühl M, Kestler HA (2007) Extended analyses of the Wnt/beta-catenin pathway: robustness and oscillatory behaviour. FEBS letters 581: 4043– 4048. 17678900
- [36]Kestler HA, Kühl M (2011) Generating a Wnt switch: it’s all about the right dosage. The Journal of cell biology 193: 431– 433. 21536746 PMC3087014
- [37]Turing AM (1952) The Chemical Basis of Morphogenesis. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 237: 37– 72. PMC4360114 25750229
- [38]Gillespie DT (1977) Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry 81: 2340– 2361.
- [39]Kestler HA, Kühl M (2008) From individual Wnt pathways towards a Wnt signalling network. Philosophical Transactions of the Royal Society of London Series B, Biological sciences 363: 1333– 1347. 18192173 PMC2610122
- [40]Fauré A, Naldi A, Chaouiya C, Thieffry D (2006) Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22: e124– e131. 16873462
- [41]Albert R, Othmer HG (2003) The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. Journal of Theoretical Biology 223: 1– 18. 12782112 PMC6388622
- [42]Giacomantonio CE, Goodhill GJ (2010) A Boolean Model of the Gene Regulatory Network Underlying Mammalian Cortical Area Development. PLoS Comput Biol 6: e1000936. 20862356 PMC2940723
- [43]Bornholdt S (2005) Systems biology. Less is more in modeling large genetic networks. Science 310: 449– 451. 16239464
- [44]Bornholdt S (2008) Boolean network models of cellular regulation: prospects and limitations. Journal of the Royal Society, Interface 5 Suppl 1 S85– 94. PMC2386560 18508746
- [45]Hopfensitz M, Müssel C, Wawra C, Maucher M, Kühl M, et al (2011) Multiscale Binarization of Gene Expression Data for Reconstructing Boolean Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9: 487– 498. 21464514
- [47]Maucher M, Kracher B, Kühl M, Kestler HA (2011) Inferring Boolean network structure via correlation. Bioinformatics 27: 1529– 1536. 21471013
- [48]Ghysen A, Thomas R (2003) The formation of sense organs in Drosophila: a logical approach. BioEssays: news and reviews in molecular, cellular and developmental biology 25: 802– 807. 12879451
- [49]Espinosa-Soto C, Padilla-Longoria P, Alvarez-Buylla ER (2004) A Gene Regulatory Network Model for Cell-Fate Determination during Arabidopsis thaliana Flower Development That Is Robust and Recovers Experimental Gene Expression Profiles. The Plant Cell 16: 2923– 2939. 15486106 PMC527189
- [50]Kestler HA, Wawra C, Kracher B, Kühl M (2008) Network modeling of signal transduction: establishing the global view. BioEssays 30: 1110– 1125. 18937364
- [51]Müssel C, Hopfensitz M, Kestler HA (2010) BoolNet - an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 26: 1378– 1380. 20378558
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Nim, H. T., Dang, L., Thiyagarajah, H., Bakopoulos, D., See, M., Charitakis, N., Sibbritt, T., Eichenlaub, M. P., Archer, S. K., Fossat, N., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02539-0 · Cited by 11
Metadata
- Authors
- Herrmann, F., Groß, A., Zhou, D., Kestler, H. A., & Kühl, M.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-10-02
- Volume
- 7
- Issue
- 10
- Pages
- e46798
- ISSN
- 1932-6203
- PMC
- PMC3462786
- Cited by
- 79
- References
- 1
- Language
- en
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