Abstract
Salt stress adversely affects plant growth and productivity worldwide. Overcoming the defects of profiling analyses caused by heterogeneity of technical variations in individual studies and prediction of salt stress response key genes and pathways are conducive to mine potential salt responses mechanisms and of great interest for agricultural research. In this research, a literature-searching strategy was used to identify salt stress response expression profiling studies in Arabidopsis from the PubMed database, the Gene Expression Omnibus (GEO) database, and the ArrayExpress database. Twenty-five studies were filtered from the 2161, 121, and 700 identified studies. A rank aggregation method (RRA)-based meta-analysis were conducted to synthesize the 25 profiling datasets and identified 829 dysregulated genes with 452 up-regulated and 377 down-regulated in NaCl-treated samples. Gene ontology enrichment and pathway analyses classified the 452 up-regulated genes into functional categories involved “response to plant hormone and compounds,” “signaling” and “developmental plasticity,” etc. In total, 111 dysregulated transcription factors (TFs) were further identified and 387 differentially expressed genes (DEGs) were predicted as these TFs’ targets. The identification of transcriptional factors, functional repertoire, and biological pathways response to the salt stress signal would promote mechanistic studies underlying stress tolerance process in Arabidopsis at systematic level and would contribute to discover the conservation and diversification of stress resistance and adaptation abilities of various plants during the evolution of plant kingdom.
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Acknowledgements
This work was supported by Natural Science Foundation of China (31470298), the Science and Technology Development Foundation of Shandong Province (2010GSF10205), the Ministry of Science and Technology of China (2011CB944604) and the Science and Technology Commission of Shanghai Municipality (14DZ 2260400).
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Online Resource 1
Zhang_et_al_ESM_1.xlsx, information of the re-analyzed samples of four studies (XLSX 13 kb)
Online Resource 2
Zhang_et_al_ESM_2.xlsx, the differently expressed genes reported in the 25 researches (XLSX 467 kb)
Online Resource 3
Zhang_et_al_ESM_3.xlsx, the dysregulated genes was significantly identified by RRA (XLSX 57 kb)
Online Resource 4
Zhang_et_al_ESM_4.xlsx, the gene ontology enrichment results for the dysregulated genes (XLSX 30 kb)
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Zhang_et_al_ESM_5.xlsx, information of the screened dysregulated TFs and their targets (XLSX 155 kb)
Online Resource 6
Zhang_et_al_ESM_6.xlsx, the comparing result of GO enrichment analysis of these genes and the functional verified salt stress response genes (XLSX 50 kb)
Information on Electronic Supplementary Material
Information on Electronic Supplementary Material
Online Resource 1. Information of the re-analyzed samples of four studies.
Online Resource 2. The differently expressed genes reported in the 25 researches.
Online Resource 3. Dysregulated genes was significantly identified by RRA.
Online Resource 4. The gene ontology enrichment results for the dysregulated genes.
Online Resource 5. Information of the screened dysregulated TFs and their targets.
Online Resource 6. The comparing result of GO enrichment analysis of these genes and the functional verified salt stress response genes.
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Zhang, L., Zhang, X. & Fan, S. Meta-analysis of salt-related gene expression profiles identifies common signatures of salt stress responses in Arabidopsis . Plant Syst Evol 303, 757–774 (2017). https://doi.org/10.1007/s00606-017-1407-x
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DOI: https://doi.org/10.1007/s00606-017-1407-x