气候变化领域集成服务门户(CCPortal): Protein structure-based gene expression signatures

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DOI	10.1073/pnas.2014866118
	Protein structure-based gene expression signatures
	Rahman R.; Zatorski N.; Hansen J.; Xiong Y.; Van Hasselt J.G.C.; Sobie E.A.; Birtwistle M.R.; Azeloglu E.U.; Iyengar R.; Schlessinger A.
发表日期	2021
ISSN	0027-8424
卷号	118 期号:19
英文摘要	Gene expression signatures (GES) connect phenotypes to differential messenger RNA (mRNA) expression of genes, providing a powerful approach to define cellular identity, function, and the effects of perturbations. The use of GES has suffered from vague assessment criteria and limited reproducibility. Because the structure of proteins defines the functional capability of genes, we hypothesized that enrichment of structural features could be a generalizable representation of gene sets. We derive structural gene expression signatures (sGES) using features from multiple levels of protein structure (e.g., domain and fold) encoded by the mRNAs in GES. Comprehensive analyses of data from the Genotype-Tissue Expression Project (GTEx), the all RNA-seq and ChIP-seq sample and signature search (ARCHS4) database, and mRNA expression of drug effects on cardiomyocytes show that sGES are useful for characterizing biological phenomena. sGES enable phenotypic characterization across experimental platforms, facilitates interoperability of expression datasets, and describe drug action on cells. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Gene expression signatures; Reproducibility; Structural bioinformatics
语种	英语
scopus关键词	messenger RNA; adult; Article; cardiac muscle cell; chromatin immunoprecipitation sequencing; controlled study; deep learning; functional genomics; gene expression; gene expression signature; genotype; human; human cell; phenotype; priority journal; protein domain; protein folding; protein structure; quantitative analysis; reproducibility; RNA sequence; sensitivity and specificity; transcriptomics
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/238576
作者单位	Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, United States; Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
推荐引用方式 GB/T 7714	Rahman R.,Zatorski N.,Hansen J.,et al. Protein structure-based gene expression signatures[J],2021,118(19).
APA	Rahman R..,Zatorski N..,Hansen J..,Xiong Y..,Van Hasselt J.G.C..,...&Schlessinger A..(2021).Protein structure-based gene expression signatures.Proceedings of the National Academy of Sciences of the United States of America,118(19).
MLA	Rahman R.,et al."Protein structure-based gene expression signatures".Proceedings of the National Academy of Sciences of the United States of America 118.19(2021).