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iNID: An Analytical Framework for Identifying Network Models for Interplays among Developmental Signaling in Arabidopsis

Title
iNID: An Analytical Framework for Identifying Network Models for Interplays among Developmental Signaling in Arabidopsis
Authors
Choi, D[Choi, Daeseok]Choi, J[Choi, Jaemyung]Kang, B[Kang, Byeongsoo]Lee, S[Lee, Seungchul]Cho, YH[Cho, Young-hyun]Hwang, I[Hwang, Ildoo]Hwang, D[Hwang, Daehee]
DGIST Authors
Hwang, D[Hwang, Daehee]
Issue Date
2014-05
Citation
Molecular Plant, 7(5), 792-813
Type
Article
Article Type
Article
Keywords
ArabidopsisBiological ModelBiologyBrassinosteroidBrassinosteroidsComputational BiologyCyclopentane DerivativeCyclopentanesCytokininCytokininsCytologyDatabases, GeneticDevelopmentDNA, PlantDrug EffectsEthyleneEthylene DerivativeEthylenesGenetic DatabaseGeneticsGrowth, Development and AgingIndoleacetic Acid DerivativeIndoleacetic AcidsInternetJasmonic AcidLightMetabolismModels, BiologicalNetwork AnalysisOxylipinOxylipinsPhysiological StressPlant DNAPlant ProteinsProceduresProtein AnalysisProtein Interaction MappingRadiation ResponseSalicylic AcidSignal InterplaysSignal TransductionStress, PhysiologicalTranscriptomeTranscriptome AnalysisVegetable Protein
ISSN
1674-2052
Abstract
Integration of internal and external cues into developmental programs is indispensable for growth and development of plants, which involve complex interplays among signaling pathways activated by the internal and external factors (IEFs). However, decoding these complex interplays is still challenging. Here, we present a web-based platform that identifies key regulators and Network models delineating Interplays among Developmental signaling (iNID) in Arabidopsis. iNID provides a comprehensive resource of (1) transcriptomes previously collected under the conditions treated with a broad spectrum of IEFs and (2) protein and genetic interactome data in Arabidopsis. In addition, iNID provides an array of tools for identifying key regulators and network models related to interplays among IEFs using transcriptome and interactome data. To demonstrate the utility of iNID, we investigated the interplays of (1) phytohormones and light and (2) phytohormones and biotic stresses. The results revealed 34 potential regulators of the interplays, some of which have not been reported in association with the interplays, and also network models that delineate the involvement of the 34 regulators in the interplays, providing novel insights into the interplays collectively defined by phytohormones, light, and biotic stresses. We then experimentally verified that BME3 and TEM1, among the selected regulators, are involved in the auxin-brassinosteroid (BR)-blue light interplay. Therefore, iNID serves as a useful tool to provide a basis for understanding interplays among IEFs. © The Author 2013.
URI
http://hdl.handle.net/20.500.11750/3092
DOI
10.1093/mp/sst173
Publisher
Cell Press
Related Researcher
  • Author Hwang, Dae Hee Systems Biology and Medicine Lab
  • Research Interests Multilayered spatiotemporal networks; Regulatory motifs or pathways; Metabolite-protein networks; Network stochasticity; Proteomics and informatics
Files:
There are no files associated with this item.
Collection:
New BiologyETC1. Journal Articles


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