气候变化领域集成服务门户(CCPortal): Predicting transcriptional responses to cold stress across plant species

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DOI	10.1073/pnas.2026330118
	Predicting transcriptional responses to cold stress across plant species
	Meng X.; Liang Z.; Dai X.; Zhang Y.; Mahboub S.; Ngu D.W.; Roston R.L.; Schnable J.C.
发表日期	2021
ISSN	00278424
卷号	118 期号:10
英文摘要	Although genome-sequence assemblies are available for a growing number of plant species, gene-expression responses to stimuli have been cataloged for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification model to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained by using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species provided at least equivalent performance to models trained and tested in a single species and outperformed single-species models in cross-species prediction. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene-expression patterns in related, less-studied species with sequenced genomes. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Cold stress; Comparative genomics; Machine learning; Transcriptional regulation
语种	英语
scopus关键词	article; chromatin; classifier; cold stress; comparative genomics; genetic transcription; human; prediction
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/180326
作者单位	Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, NE 68588, United States; Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE 68588, United States; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, 273100, China; Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE 68588, United States
推荐引用方式 GB/T 7714	Meng X.,Liang Z.,Dai X.,et al. Predicting transcriptional responses to cold stress across plant species[J],2021,118(10).
APA	Meng X..,Liang Z..,Dai X..,Zhang Y..,Mahboub S..,...&Schnable J.C..(2021).Predicting transcriptional responses to cold stress across plant species.Proceedings of the National Academy of Sciences of the United States of America,118(10).
MLA	Meng X.,et al."Predicting transcriptional responses to cold stress across plant species".Proceedings of the National Academy of Sciences of the United States of America 118.10(2021).