SEGN: Inferring real-time gene networks mediating phenotypic plasticity

Computational and Structural Biotechnology Journal - Tập 18 - Trang 2510-2521 - 2020
Libo Jiang1,2, Christopher H. Griffin3, Rongling Wu1,2,4
1Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
2Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
3Applied Research Laboratory, The Pennsylvania State University, University Park, PA, 16802, USA
4Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA 17033, USA

Tài liệu tham khảo

Bradshaw, 1965, Evolutionary significance of phenotypic plasticity in plants, Adv Genet, 13, 115, 10.1016/S0065-2660(08)60048-6 Via, 1985, Genotype-environment interaction and the evolution of phenotypic plasticity, Evolution, 39, 505, 10.2307/2408649 Gomulkiewicz, 1992, Quantitative genetics and the evolution of reaction norms, Evolution, 46, 390, 10.2307/2409860 Gavrilets, 1993, The genetics of phenotypic plasticity. V. Evolution of reaction norm shape, J Evol Biol, 6, 31, 10.1046/j.1420-9101.1993.6010031.x Lande, 2009, Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation, J Evol Biol, 22, 1435, 10.1111/j.1420-9101.2009.01754.x Lande, 2014, Evolution of phenotypic plasticity and environmental tolerance of a labile quantitative character in a fluctuating environment, J Evol Biol, 27, 866, 10.1111/jeb.12360 West-Eberhard, 2003 Aubin-Horth, 2009, Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity, Mol Ecol, 18, 3763, 10.1111/j.1365-294X.2009.04313.x Moczek, 2011, The role of developmental plasticity in evolutionary innovation, Proc Biol Sci, 278, 2705 Wu, 1998, The detection of plasticity genes in heterogeneous environments, Evolution, 52, 867, 10.2307/2411229 Zhai, 2014, A synthetic framework for modeling the genetic basis of phenotypic plasticity and its costs, New Phytol, 201, 357, 10.1111/nph.12458 Badisco, 2011, Microarray-based transcriptomic analysis of differences between long-term gregarious and solitarious desert locusts, PLoS ONE, 2011 Schunter, 2014, Transcriptome analyses and differential gene expression in a non-model fish species with alternative mating tactics, BMC Genomics, 15, 167, 10.1186/1471-2164-15-167 Alvarez, 2015, Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?, Mol Ecol, 24, 710, 10.1111/mec.13055 Colbourne, 2011, The ecoresponsive genome of Daphnia pulex, Science, 2011, 555, 10.1126/science.1197761 Schneider, 2014, Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish, Mol Ecol, 23, 4511, 10.1111/mec.12851 van Gestel, 2016, Regulatory mechanisms link phenotypic plasticity to evolvability, Sci Rep, 6, 24524, 10.1038/srep24524 Lafuente, 2019, Genomics of developmental plasticity in animals, Front Genet, 10, 720, 10.3389/fgene.2019.00720 Pfennig, 2014, Towards a gene regulatory network perspective on phenotypic plasticity, genetic accommodation and genetic assimilation, Mol Ecol, 23, 4438, 10.1111/mec.12887 Sikkink, 2019, Environmental and evolutionary drivers of the modular gene regulatory network underlying phenotypic plasticity for stress resistance in the Nematode Caenorhabditis remanei, G3 (Bethesda), 9, 969, 10.1534/g3.118.200017 Chettaoui, 2006, Rewriting game theory as a foundation for state-based models of gene regulation, 257 Moretti, 2010, Using coalitional games on biological networks to measure centrality and power of genes, Bioinformatics, 26, 2721, 10.1093/bioinformatics/btq508 Moretti, 2010, An overview of recent applications of game theory to bioinformatics, Inform Sci, 180, 4312, 10.1016/j.ins.2010.07.019 Smith, 1973, The logic of animal conflict, Nature, 246, 15, 10.1038/246015a0 Kim, 2008, A computational approach to the functional clustering of periodic gene expression profiles, Genetics, 180, 821, 10.1534/genetics.108.093690 Wang, 2012, How to cluster gene expression dynamics in response to environmental signals, Brief Bioinform, 13, 162, 10.1093/bib/bbr032 Jiang, 2014, A skellam model to identify differential patterns of gene expression induced by environmental signals, BMC Genomics, 15, 772, 10.1186/1471-2164-15-772 Tibshirani, 1996, Regression shrinkage and selection via the LASSO, J Roy Stat Soc B, 58, 267 Li, 2005, Structural characteristics and eco-adaptability of heteromorphic leaves of Populus euphratica, Forest Ecosys, 7, 11 Liu, 2015, Epidermal micromorphology and mesophyll structure of Populus euphratica heteromorphic leaves at different development stages, PLoS ONE, 10, 10.1145/2818302 Wang, 2015, Root plasticity of Populus euphratica seedlings in response to different water table depths and contrasting sediment types, PLoS ONE, 10 von Neumann, 1946 Nash, 1950, Equilibrium points in n-person games, Proc Natl Acad Sci USA, 36, 48, 10.1073/pnas.36.1.48 Fisher, 1930 Michailidis, 2013, Autoregressive models for gene regulatory network inference: Sparsity, stability and causality issues, Math Biosci, 246, 326, 10.1016/j.mbs.2013.10.003 Callebaut, 2009 Dunbar, 1992, Neocortex size as a constraint on group size in primates, J Hum Evol, 22, 469, 10.1016/0047-2484(92)90081-J Horvath, 2008, Geometric interpretation of gene coexpression network analysis, PLoS Comput Biol, 4, 10.1371/journal.pcbi.1000117 Jin, 2015, An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors, Mol Biol Evol, 32, 1767, 10.1093/molbev/msv058 Zhu, 2016, Abiotic stress signaling and responses in plants, Cell, 167, 313, 10.1016/j.cell.2016.08.029 Rushton, 2010, WRKY transcription factors, Trends Plant Sci, 5, 247, 10.1016/j.tplants.2010.02.006 Blake, 2015, Gene Ontology Consortium: going forward, Nuclei Acids Res, 431049 Malinovsky, 2014, Antagonistic regulation of growth and immunity by the Arabidopsis basic helix-loop-helix transcription factor homolog of brassinosteroid enhanced expression2 interacting with increased leaf inclination1 binding bHLH1, Plant Physiol, 164, 1443, 10.1104/pp.113.234625 Guo, 2003, Plant responses to ethylene gas are mediated by SCF EBF1/EBF2-dependent proteolysis of EIN3 transcription factor, Cell, 115, 667, 10.1016/S0092-8674(03)00969-3 Chen, 2001, A superfamily of proteins with novel cysteine-rich repeats, Plant Physiol, 126, 473, 10.1104/pp.126.2.473 Lèbre, 2009, Inferring dynamic genetic networks with low order independencies, Stat Appl Genet Mol Biol, 8, 1, 10.2202/1544-6115.1294 Wu, 2014, Sparse additive ordinary differential equations for dynamic gene regulatory network modeling, J Am Stat Assoc, 109, 700, 10.1080/01621459.2013.859617 Major, 2008, Functional analysis of the Kunitz trypsin inhibitor family in poplar reveals biochemical diversity and multiplicity in defense against herbivores, Plant Physiol, 146, 888, 10.1104/pp.107.106229 Licausi, 2013, APETALA 2/Ethylene Responsive Factor (AP 2/ERF) transcription factors: Mediators of stress responses and developmental programs, New Phytol, 199, 639, 10.1111/nph.12291 Freeman, 1978, Centrality in social networks conceptual clarification, Social Networks, 1, 215, 10.1016/0378-8733(78)90021-7 Brandes, 2001, A faster algorithm for betweenness centrality, J Math Sociol, 25, 163, 10.1080/0022250X.2001.9990249 Hage, 1995, Eccentricity and centrality in networks, Social Networks, 17, 57, 10.1016/0378-8733(94)00248-9 Bonacich, 2007, Some unique properties of eigenvector centrality, Social Networks, 29, 555, 10.1016/j.socnet.2007.04.002 Page, 1998, The PageRank Citation Ranking: Bringing Order to the Web, Stanford Digital Librar Work Paper, 9, 1 Lavarenne, 2018, The spring of systems biology-driven breeding, Trends Plant Sci, 23, 706, 10.1016/j.tplants.2018.04.005 Julkowska, 2015, Tuning plant signaling and growth to survive salt, Trends Plant Sci, 20, 586, 10.1016/j.tplants.2015.06.008 Munns, 2015, Salinity tolerance of crops - what is the cost?, New Phytol, 208, 668, 10.1111/nph.13519 Mooney, 2016, Phenotypic plasticity in prostate cancer: role of intrinsically disordered proteins, Asian J Andrology, 18, 704, 10.4103/1008-682X.183570 Varankar, 2020, Functional balance between TCF21-Slug defines cellular plasticity and sub-classes in high-grade serous ovarian cancer, Carcinogenesis, 41, 515, 10.1093/carcin/bgz119