T. R. Golub, D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek et al., Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring, Science, vol.286, issue.5439, pp.531-538, 1999.

A. De-la-fuente, From 'differential expression' to 'differential networking' -identification of dysfunctional regulatory networks in diseases, Trends Genet, vol.26, issue.7, pp.326-359, 2010.

R. Sharan and T. Ideker, Modeling cellular machinery through biological network comparison, Nat Biotechnol, vol.24, issue.4, pp.427-460, 2006.

T. Ideker and N. J. Krogan, Differential network biology, Mol Syst Biol, vol.8, p.565, 2012.

T. Ideker, O. Ozier, B. Schwikowski, and A. F. Siegel, Discovering regulatory and signalling circuits in molecular interaction networks, Bioinformatics, vol.18, issue.suppl_1, p.233, 2002.

F. E. Faisal and T. Milenkovi?, Dynamic networks reveal key players in aging, Bioinformatics, vol.30, issue.12, p.1721, 2014.

M. Bansal, V. Belcastro, A. Ambesi-impiombato, D. Bernardo, and D. , How to infer gene networks from expression profiles, Mol Syst Biol, vol.3, issue.1, p.78, 2007.

G. Altay and F. Emmert-streib, Inferring the conservative causal core of gene regulatory networks, BMC Syst Biol, vol.4, issue.1, p.132, 2010.

D. Marbach, J. C. Costello, R. Küffner, N. M. Vega, R. J. Prill et al., Wisdom of crowds for robust gene network inference, Nat Methods, vol.9, issue.8, pp.796-804, 2012.

S. Friedel, B. Usadel, N. Von-wiren, and N. Sreenivasulu, Reverse Engineering: A Key Component of Systems Biology to Unravel Global Abiotic Stress Cross-Talk, Front Plant Sci, vol.3, p.294, 2012.

A. Barabási, N. Gulbahce, and J. Loscalzo, Network Medicine: A Network-based Approach to Human Disease, Nat Rev Genet, vol.12, issue.1, pp.56-68, 2011.

G. Altay, M. Asim, F. Markowetz, and D. E. Neal, Differential C3net reveals disease networks of direct physical interactions, BMC Bioinformatics, vol.12, issue.1, p.296, 2011.

M. Bockmayr, F. Klauschen, B. Györffy, C. Denkert, and J. Budczies, New network topology approaches reveal differential correlation patterns in breast cancer, BMC Syst Biol, vol.7, p.78, 2013.

G. Warsow, B. Greber, S. Falk, C. Harder, M. Siatkowski et al., Expressencerevealing the essence of differential experimental data in the context of an interaction/regulation net-work, BMC Syst Biol, vol.4, p.164, 2010.

P. Langfelder, R. Luo, M. C. Oldham, and S. Horvath, Is my network module preserved and reproducible?, PLOS Comput Biol, vol.7, issue.1, pp.1-29, 2011.

V. Pelechano and L. M. Steinmetz, Gene regulation by antisense transcription, Nat Rev Genet, vol.14, issue.12, pp.880-93, 2013.

B. Gelfand, J. Mead, A. Bruning, N. Apostolopoulos, V. Tadigotla et al., Regulated antisense transcription controls expression of cell-type-specific genes in yeast, Mol Cell Biol, vol.31, issue.8, pp.1701-1710, 2011.

M. A. Faghihi, M. Zhang, J. Huang, F. Modarresi, M. P. Van-der-brug et al., Evidence for natural antisense transcript-mediated inhibition of microRNA function, Genome Biol, vol.11, p.56, 2010.

C. Carrieri, L. Cimatti, M. Biagioli, A. Beugnet, S. Zucchelli et al., Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat, Nature, vol.491, issue.7424, pp.454-461, 2012.

S. C. Murray, S. Haenni, F. S. Howe, H. Fischl, K. Chocian et al., Sense and antisense transcription are associated with distinct chromatin architectures across genes, Nucleic Acids Re, vol.43, issue.16, pp.7823-7860, 2015.

H. Yi and E. J. Richards, A Cluster of Disease Resistance Genes in Arabidopsis Is Coordinately Regulated by Transcriptional Activation and RNA Silencing, Plant Cell, vol.19, issue.9, pp.2929-2968, 2007.

O. Borsani, J. Zhu, P. E. Verslues, R. Sunkar, and J. Zhu, Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis, Cell, vol.123, issue.7, pp.1279-91, 2005.

H. Wang, P. J. Chung, J. Liu, I. Jang, M. Kean et al., Genomewide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis, Genome Res, pp.2014165555-113

J. Celton, S. Gaillard, M. Bruneau, S. Pelletier, S. Aubourg et al., Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control, New Phytol, vol.203, issue.1, pp.287-99, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01209978

B. C. Meyers, T. H. Vu, S. S. Tej, H. Ghazal, M. Matvienko et al., Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing, Nat Biotechnol, vol.22, issue.8, pp.1006-1017, 2004.

V. Stolc, M. P. Samanta, W. Tongprasit, H. Sethi, S. Liang et al., Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays, Proc Natl Acad Sci, vol.102, issue.12, pp.4453-4461, 2005.

A. A. Margolin, I. Nemenman, K. Basso, C. Wiggins, G. Stolovitzky et al., ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context, BMC Bioinformatics, vol.7, issue.1, p.7, 2006.

X. Zhang, K. Liu, Z. Liu, B. Duval, J. Richer et al., NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference, Bioinformatics, vol.29, issue.1, pp.106-119, 2013.

R. Velasco, A. Zharkikh, J. Affourtit, A. Dhingra, A. Cestaro et al., Nat Genet, vol.42, issue.10, pp.833-842, 2010.

J. H. Bullard, E. Purdom, K. D. Hansen, and S. Dudoit, Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments, BMC Bioinformatics, vol.11, p.94, 2010.

X. Qiu, H. Wu, and R. Hu, The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis, BMC Bioinformatics, vol.14, p.124, 2013.

M. Legeay, B. Duval, and J. Renou, Differential Functional Analysis and Change Motifs in Gene Networks to Explore the Role of Anti-sense Transcription, Bioinformatics Research and Applications. Lecture Notes in Computer Science. Switzerland, pp.117-126, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01412515

, The Gene Ontology Consortium: Expansion of the Gene Ontology knowledgebase and resources, Nucleic Acids Res, vol.45, issue.D1, pp.331-339, 2017.

, The Arabidopsis Information Resource (TAIR), 2017.

S. Maere, K. Heymans, and M. Kuiper, BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks, Bioinformatics, vol.21, issue.16, pp.3448-3457, 2005.

P. Langfelder and S. Horvath, WGCNA: an R package for weighted correlation network analysis, BMC Bioinformatics, vol.9, issue.1, p.559, 2008.

R. Steuer, J. Kurths, C. O. Daub, J. Weise, and J. Selbig, The mutual information: Detecting and evaluating dependencies between variables, Bioinformatics, vol.18, issue.2, pp.231-271, 2002.

Z. Kurt, N. Aydin, and G. Altay, A comprehensive comparison of association estimators for gene network inference algorithms, Bioinformatics, vol.30, issue.15, pp.2142-2151, 2014.

S. S. Shen-orr, M. R. Mangan, S. Alon, and U. , Network motifs in the transcriptional regulation network of Escherichia coli, Nat Genet, vol.31, issue.1, pp.64-68, 2002.

H. Ma, B. Kumar, U. Ditges, F. Gunzer, J. Buer et al., An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs, Nucleic Acids Res, vol.32, issue.22, pp.6643-6652, 2004.

N. Guelzim, S. Bottani, P. Bourgine, and F. Képès, Topological and causal structure of the yeast transcriptional regulatory network, Nat Genet, vol.31, issue.1, pp.60-63, 2002.

B. Tvd, K. V. Leemput, B. Naudts, R. Pv, H. Ma et al., SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms, BMC Bioinformatics, vol.7, issue.1, p.43, 2006.

M. Legeay, B. Duval, J. Renou, T. -p-;-tian, Q. Jiang et al., Inference and differential analysis of extended core networks: A way to study anti-sense regulation, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, pp.284-291, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01467169

M. T. Dittrich, G. W. Klau, A. Rosenwald, T. Dandekar, and T. Müller, Identifying functional modules in protein-protein interaction networks: an integrated exact approach, Bioinformatics, vol.24, issue.13, pp.223-254, 2008.

A. Sadeghi and H. Fröhlich, Steiner tree methods for optimal sub-network identification: an empirical study, BMC Bioinformatics, vol.14, p.144, 2013.

R. M. Karp, Reducibility among Combinatorial Problems, Complexity of Computer Computations. The IBM Research Symposia Series, pp.85-103, 1972.

P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang et al., Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks, Genome Res, vol.13, issue.11, pp.2498-504, 2003.

J. W. Johnston, E. W. Hewett, and M. Hertog, Postharvest softening of apple (Malus domestica) fruit: A review, New Zealand J Crop Hortic Sci, vol.30, issue.3, pp.145-60, 2002.

Q. Yang, J. Rao, S. Yi, K. Meng, J. Wu et al., Antioxidant enzyme activity and chilling injury during low-temperature storage of Kiwifruit cv. Hongyang exposed to gradual postharvest cooling, Hortic Environ Biotechnol, vol.53, issue.6, pp.505-517, 2012.

N. Chaparzadeh and B. Yavari, Antioxidant responses of Golden delicious apple under cold storage conditions, Iran J Plant Physiol, vol.4, issue.1, pp.907-922, 2013.

I. Juszczak, J. Cvetkovic, E. Zuther, D. K. Hincha, and M. Baier, Natural Variation of Cold Deacclimation Correlates with Variation of Cold-Acclimation of the Plastid Antioxidant System in Arabidopsis thaliana Accessions, Front Plant Sci, vol.7, p.305, 2016.

Y. Zhang, B. Zhang, D. Yan, W. Dong, W. Yang et al., Two Arabidopsis cytochrome P450 monooxygenases, CYP714a1 and CYP714a2, function redundantly in plant development through gibberellin deactivation, Plant J Cell Mol Biol, vol.67, issue.2, pp.342-53, 2011.

E. Issakidis-bourguet, N. Mouaheb, Y. Meyer, and M. Miginiac-maslow, Heterologous complementation of yeast reveals a new putative function for chloroplast m-type thioredoxin, Plant J Cell Mol Biol, vol.25, issue.2, pp.127-162, 2001.

W. Tang, T. Kim, J. A. Oses-prieto, Y. Sun, Z. Deng et al., BSKs mediate signal transduction from the receptor kinase BRI1 in Arabidopsis, Science, vol.321, issue.5888, pp.557-60, 2008.

S. D. Clouse and J. M. Sasse, BRASSINOSTEROIDS: Essential Regulators of Plant Growth and Development, Annu Rev Plant Physiol Plant Mol Biol, vol.49, pp.427-51, 1998.

Y. Shi, A. L. Li, X. Huang, C. Chen, and G. , The octadecanoid signaling pathway participates in the chilling-induced transcription of ?-3 fatty acid desaturases in Arabidopsis, Plant Physiol Biochem, vol.49, issue.2, pp.208-223, 2011.

R. Iglesias-fernández, C. Barrero-sicilia, N. Carrillo-barral, L. Oñate-sánchez, and P. Carbonero, Arabidopsis thaliana bZIP44: a transcription factor affecting seed germination and expression of the mannanase-encoding gene AtMAN7, Plant J Cell Mol Biol, vol.74, issue.5, pp.767-80, 2013.

F. Weltmeier, F. Rahmani, A. Ehlert, K. Dietrich, K. Schütze et al., Expression patterns within the Arabidopsis C/S1 bZIP transcription factor network: availability of heterodimerization partners controls gene expression during stress response and development, Plant Mol Bio, vol.69, issue.1-2, pp.107-126, 2009.

S. Hwang, H. Li, H. Alavilli, B. Lee, and D. Choi, Molecular and physiological characterization of AtHIGD1 in Arabidopsis, Biochem Biophys Res Commun, vol.487, issue.4, pp.881-86, 2017.

B. Liu, L. Sun, L. Ma, and F. Hao, Both AtrbohD and AtrbohF are essential for mediating responses to oxygen deficiency in Arabidopsis, Plant Cell Rep, vol.36, issue.6, pp.947-57, 2017.

H. Li, K. Ye, Y. Shi, J. Cheng, X. Zhang et al., BZR1 Positively Regulates Freezing Tolerance via CBF-Dependent and CBF-Independent Pathways in Arabidopsis, Mol Plant, vol.10, issue.4, pp.545-59, 2017.

J. Y. Kim, W. Y. Kim, K. J. Kwak, S. H. Oh, Y. S. Han et al., Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process, J Exp Bot, vol.61, issue.9, pp.2317-2342, 2010.

B. Lee, H. Lee, L. Xiong, and J. Zhu, A Mitochondrial Complex I Defect Impairs Cold-Regulated Nuclear Gene Expression, Plant Cell, vol.14, issue.6, pp.1235-51, 2002.

Y. Oono, M. Seki, M. Satou, K. Iida, K. Akiyama et al., Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays, Funct Integr Genom, vol.6, issue.3, pp.212-246, 2006.

R. B. Nair, K. L. Bastress, M. O. Ruegger, J. W. Denault, and C. Chapple, The Arabidopsis thaliana REDUCED EPIDERMAL FLUORESCENCE1 gene encodes an aldehyde dehydrogenase involved in ferulic acid and sinapic acid biosynthesis, Plant Cell, vol.16, issue.2, pp.544-54, 2004.

J. M. Sasse, Physiological Actions of Brassinosteroids: An Update, J Plant Growth Regul, vol.22, issue.4, pp.276-88, 2003.

P. Krishna, Brassinosteroid-Mediated Stress Responses, J Plant Growth Regul, vol.22, issue.4, pp.289-97, 2003.

A. Bajguz and S. Hayat, Effects of brassinosteroids on the plant responses to environmental stresses, Plant Physiol Biochem, vol.47, issue.1, pp.1-8, 2009.

B. Li, C. Zhang, B. Cao, G. Qin, W. Wang et al., Brassinolide enhances cold stress tolerance of fruit by regulating plasma membrane proteins and lipids, Amino Acids, vol.43, issue.6, pp.2469-80, 2012.

G. M. Symons, C. Davies, Y. Shavrukov, I. B. Dry, J. B. Reid et al., Grapes on Steroids, Brassinosteroids Are Involved in Grape Berry Ripening, Plant Physiol, vol.140, issue.1, pp.150-158, 2006.

F. Q. Fu, W. H. Mao, K. Shi, Y. H. Zhou, T. Asami et al., A role of brassinosteroids in early fruit development in cucumber, J Exp Bot, vol.59, issue.9, pp.2299-308, 2008.