title: iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis.
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.
authors.affiliation: School of Interdisciplinary Bioscience and Bioengineering, POSTECH, 790-784, Pohang, Republic of Korea.
authors.forename: Daeseok
authors.initials: D
authors.lastname: Choi
authors.forename: Jaemyung
authors.initials: J
authors.lastname: Choi
authors.forename: Byeongsoo
authors.initials: B
authors.lastname: Kang
authors.forename: Seungchul
authors.initials: S
authors.lastname: Lee
authors.forename: Young-hyun
authors.initials: YH
authors.lastname: Cho
authors.forename: Ildoo
authors.initials: I
authors.lastname: Hwang
authors.forename: Daehee
authors.initials: D
authors.lastname: Hwang
mesh_terms: D017360:Arabidopsis / Q000166:cytology / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism*; D060406:Brassinosteroids / Q000494:pharmacology; D019295:Computational Biology / Q000379:methods*; D003517:Cyclopentanes / Q000494:pharmacology; D003583:Cytokinins / Q000494:pharmacology; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D005030:Ethylenes / Q000494:pharmacology; D007210:Indoleacetic Acids / Q000494:pharmacology; D020407:Internet; D008027:Light; D008954:Models, Biological; D054883:Oxylipins / Q000494:pharmacology; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping; D020156:Salicylic Acid / Q000494:pharmacology; D015398:Signal Transduction / Q000187:drug effects / Q000528:radiation effects; D013312:Stress, Physiological / Q000187:drug effects / Q000528:radiation effects; D059467:Transcriptome / Q000187:drug effects / Q000528:radiation effects
chemical_list: D060406:Brassinosteroids; D003517:Cyclopentanes; D003583:Cytokinins; D018744:DNA, Plant; D005030:Ethylenes; D007210:Indoleacetic Acids; D054883:Oxylipins; D010940:Plant Proteins; C011006:jasmonic acid; C036216:ethylene; D020156:Salicylic Acid
keywords: Arabidopsis.; development; network analysis; signal interplays; transcriptome analysis