Abstract
Phytohormones regulate diverse aspects of plant growth and environmental responses. Recent high-throughput technologies have promoted a more comprehensive profiling of genes regulated by different hormones. However, these omics data generally result in large gene lists that make it challenging to interpret the data and extract insights into biological significance. With the rapid accumulation of theses large-scale experiments, especially the transcriptomic data available in public databases, a means of using this information to explore the transcriptional networks is needed. Different platforms have different architectures and designs, and even similar studies using the same platform may obtain data with large variances because of the highly dynamic and flexible effects of plant hormones; this makes it difficult to make comparisons across different studies and platforms. Here, we present a web server providing gene set-level analyses of Arabidopsis thaliana hormone responses. GSHR collected 333 RNA-seq and 1,205 microarray datasets from the Gene Expression Omnibus, characterizing transcriptomic changes in Arabidopsis in response to phytohormones including abscisic acid, auxin, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonic acid, salicylic acid, and strigolactones. These data were further processed and organized into 1,368 gene sets regulated by different hormones or hormone-related factors. By comparing input gene lists to these gene sets, GSHR helped to identify gene sets from the input gene list regulated by different phytohormones or related factors. Together, GSHR links prior information regarding transcriptomic changes induced by hormones and related factors to newly generated data and facilities cross-study and cross-platform comparisons; this helps facilitate the mining of biologically significant information from large-scale datasets. The GSHR is freely available at http://bioinfo.sibs.ac.cn/GSHR/.
Highlights
Phytohormones are typically small endogenous compounds regulating every aspect of plant life, from plant growth and development to responses to environmental changes (Santner and Estelle, 2009; Wolters and Jurgens, 2009; Scheres and van der Putten, 2017)
The major hormones were traditionally classified into two categories, those mainly regulating developmental processes including auxin, brassinosteroid (BR), cytokinin (CK), and gibberellic acid (GA) and strigolactones, and those regulating stress responses, including abscisic acid (ABA), ethylene (ET), jasmonic acid (JA), and salicylic acid (SA)
Detailed descriptive and statistical information about the comparisons is presented (Figures 2B–D). For those hormones regulated input gene lists, further functional exploration could be directly performed on the resulting page, including hierarchical clustering of expression pattern in response to related hormones, co-expression network, enrichment analyses of pathways, gene ontology terms and InterPro domains
Summary
Phytohormones are typically small endogenous compounds regulating every aspect of plant life, from plant growth and development to responses to environmental changes (Santner and Estelle, 2009; Wolters and Jurgens, 2009; Scheres and van der Putten, 2017). Gene Set-Level Analyses of Hormone Responses by specific receptors and further activate cascades of signaling pathways, leading to remarkable biochemical and physiological changes (Santner and Estelle, 2009; Wolters and Jurgens, 2009; Scheres and van der Putten, 2017). Wide-spread crosstalk was revealed among various phytohormone pathways in response to specific developmental or environmental changes (Depuydt and Hardtke, 2011; Robert-Seilaniantz et al, 2011; Murphy, 2015). The crosstalk happens on multiple layers of regulation, among which transcriptional control is one major component
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