Atkinson NJ, Urwin PE: The interaction of plant biotic and abiotic stresses: from genes to the field. Journal of experimental botany. 2012, 63 (10): 3523-3543. 10.1093/jxb/ers100.
Article
CAS
PubMed
Google Scholar
Wang W, Vinocur B, Altman A: Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta. 2003, 218 (1): 1-14. 10.1007/s00425-003-1105-5.
Article
CAS
PubMed
Google Scholar
Cushman JC, Bohnert HJ: Genomic approaches to plant stress tolerance. Current opinion in plant biology. 2000, 3 (2): 117-124. 10.1016/S1369-5266(99)00052-7.
Article
CAS
PubMed
Google Scholar
Mittler R: Abiotic stress, the field environment and stress combination. Trends in plant science. 2006, 11 (1): 15-19. 10.1016/j.tplants.2005.11.002.
Article
CAS
PubMed
Google Scholar
Rizhsky L, Liang H, Shuman J, Shulaev V, Davletova S, Mittler R: When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant physiology. 2004, 134 (4): 1683-1696. 10.1104/pp.103.033431.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ren H, Gao Z, Chen L, Wei K, Liu J, Fan Y, Davies WJ, Jia W, Zhang J: Dynamic analysis of ABA accumulation in relation to the rate of ABA catabolism in maize tissues under water deficit. Journal of experimental botany. 2007, 58 (2): 211-219.
Article
CAS
PubMed
Google Scholar
Gray WM: Hormonal regulation of plant growth and development. PLoS biology. 2004, 2 (9): E311-10.1371/journal.pbio.0020311.
Article
PubMed Central
PubMed
Google Scholar
Wang Y, Liu C, Li K, Sun F, Hu H, Li X, Zhao Y, Han C, Zhang W, Duan Y, et al: Arabidopsis EIN2 modulates stress response through abscisic acid response pathway. Plant molecular biology. 2007, 64 (6): 633-644. 10.1007/s11103-007-9182-7.
Article
CAS
PubMed
Google Scholar
Boavida LC, Borges F, Becker JD, Feijo JA: Whole genome analysis of gene expression reveals coordinated activation of signaling and metabolic pathways during pollen-pistil interactions in Arabidopsis. Plant physiology. 2011, 155 (4): 2066-2080. 10.1104/pp.110.169813.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi A, Inoue E, Saito K: Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. The Plant cell. 2008, 20 (8): 2160-2176. 10.1105/tpc.108.058040.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995, 270 (5235): 467-470. 10.1126/science.270.5235.467.
Article
CAS
PubMed
Google Scholar
Movahedi S, Van Bel M, Heyndrickx KS, Vandepoele K: Comparative co-expression analysis in plant biology. Plant, cell & environment. 2012, 35 (10): 1787-1798. 10.1111/j.1365-3040.2012.02517.x.
Article
CAS
Google Scholar
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al: NCBI GEO: archive for functional genomics data sets--update. Nucleic acids research. 2013, D991-995. 41 Database
Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ: An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PloS one. 2007, 2 (8): e718-10.1371/journal.pone.0000718.
Article
PubMed Central
PubMed
Google Scholar
Dash S, Van Hemert J, Hong L, Wise RP, Dickerson JA: PLEXdb: gene expression resources for plants and plant pathogens. Nucleic acids research. 2012, D1194-1201. 40 Database
Sato Y, Takehisa H, Kamatsuki K, Minami H, Namiki N, Ikawa H, Ohyanagi H, Sugimoto K, Antonio BA, Nagamura Y: RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. Nucleic acids research. 2013, D1206-1213. 41 Database
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W: GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant physiology. 2004, 136 (1): 2621-2632. 10.1104/pp.104.046367.
Article
PubMed Central
CAS
PubMed
Google Scholar
Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S: NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic acids research. 2004, D575-577. 32 Database
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, et al: Gramene 2013: comparative plant genomics resources. Nucleic acids research. 2014, D1193-1199. 42 Database
Sucaet Y, Wang Y, Li J, Wurtele ES: MetNet Online: a novel integrated resource for plant systems biology. BMC bioinformatics. 2012, 13: 267-10.1186/1471-2105-13-267.
Article
PubMed Central
PubMed
Google Scholar
Nikitin A, Egorov S, Daraselia N, Mazo I: Pathway studio--the analysis and navigation of molecular networks. Bioinformatics. 2003, 19 (16): 2155-2157. 10.1093/bioinformatics/btg290.
Article
CAS
PubMed
Google Scholar
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, et al: Arabidopsis reactome: a foundation knowledgebase for plant systems biology. The Plant cell. 2008, 20 (6): 1426-1436. 10.1105/tpc.108.057976.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jensen PA, Papin JA: Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics. 2011, 27 (4): 541-547. 10.1093/bioinformatics/btq702.
Article
CAS
PubMed
Google Scholar
Beltrame L, Bianco L, Fontana P, Cavalieri D: Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data. Bioinformatics. 2013, 29 (14): 1825-1826. 10.1093/bioinformatics/btt292.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zheng HQ, Chiang-Hsieh YF, Chien CH, Hsu BK, Liu TL, Chen CN, Chang WC: AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae. BMC genomics. 2014, 15: 196-10.1186/1471-2164-15-196.
Article
PubMed Central
PubMed
Google Scholar
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K: The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. The Plant journal: for cell and molecular biology. 2007, 50 (2): 347-363. 10.1111/j.1365-313X.2007.03052.x.
Article
CAS
Google Scholar
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003, 4 (2): 249-264. 10.1093/biostatistics/4.2.249.
Article
PubMed
Google Scholar
Gautier L, Cope L, Bolstad BM, Irizarry RA: affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004, 20 (3): 307-315. 10.1093/bioinformatics/btg405.
Article
CAS
PubMed
Google Scholar
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, et al: The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic acids research. 2012, D1202-1210. 40 Database
Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, et al: Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant & cell physiology. 2013, 54 (2): e6-10.1093/pcp/pcs183.
Article
CAS
Google Scholar
Schaeffer ML, Harper LC, Gardiner JM, Andorf CM, Campbell DA, Cannon EK, Sen TZ, Lawrence CJ: MaizeGDB: curation and outreach go hand-in-hand. Database: the journal of biological databases and curation. 2011, 2011: bar022-
Article
PubMed
Google Scholar
Kinsella RJ, Kahari A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, et al: Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database: the journal of biological databases and curation. 2011, 2011: bar030-
Article
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics. 2000, 25 (1): 25-29. 10.1038/75556.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M: Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic acids research. 2014, D199-205. 42 Database
Chien CH, Chiang-Hsieh YF, Tsou AP, Weng SL, Chang WC, Huang HD: Large-Scale Investigation of Human TF-miRNA Relations Based on Coexpression Profiles. BioMed research international. 2014, 2014: 623078-
PubMed Central
PubMed
Google Scholar
Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G: The tify family previously known as ZIM. Trends in plant science. 2007, 12 (6): 239-244. 10.1016/j.tplants.2007.04.004.
Article
CAS
PubMed
Google Scholar
Chini A, Fonseca S, Fernandez G, Adie B, Chico JM, Lorenzo O, Garcia-Casado G, Lopez-Vidriero I, Lozano FM, Ponce MR, et al: The JAZ family of repressors is the missing link in jasmonate signalling. Nature. 2007, 448 (7154): 666-671. 10.1038/nature06006.
Article
CAS
PubMed
Google Scholar
Moreno JE, Shyu C, Campos ML, Patel LC, Chung HS, Yao J, He SY, Howe GA: Negative feedback control of jasmonate signaling by an alternative splice variant of JAZ10. Plant physiology. 2013, 162 (2): 1006-1017. 10.1104/pp.113.218164.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chung HS, Howe GA: A critical role for the TIFY motif in repression of jasmonate signaling by a stabilized splice variant of the JASMONATE ZIM-domain protein JAZ10 in Arabidopsis. The Plant cell. 2009, 21 (1): 131-145. 10.1105/tpc.108.064097.
Article
PubMed Central
CAS
PubMed
Google Scholar