Large-scale mapping of mammalian transcriptomes identifies conserved   genes associated with different cell states

doi:10.1093/nar/gkw1256

CORC > 北京大学 > 生命科学学院

	Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states
	Yang, Yang ; Yang, Yu-Cheng T. ; Yuan, Jiapei ; Lu, Zhi John ; Li, Jingyi Jessica
刊名	NUCLEIC ACIDS RESEARCH
	2017
关键词	LONG NONCODING RNAS EMBRYONIC STEM-CELLS EVOLUTIONARY DYNAMICS EXPRESSION PATTERNS PARKINSONS-DISEASE HOUSEKEEPING GENES ALZHEIMERS-DISEASE BINDING PROTEINS SUPER-ENHANCERS MOUSE
DOI	10.1093/nar/gkw1256
英文摘要	Distinguishing cell states based only on gene expression data remains a challenging task. This is true even for analyses within a species. In cross-species comparisons, the results obtained by different groups have varied widely. Here, we integrate RNA-seq data from more than 40 cell and tissue types of four mammalian species to identify sets of associated genes as indicators for specific cell states in each species. We employ a statistical method, TROM, to identify both protein-coding and non-coding indicators. Next, we map the cell states within each species and also between species using these indicator genes. We recapitulate known phenotypic similarity between related cell and tissue types and reveal molecular basis for their similarity. We also report novel associations between several tissues and cell types with functional support. Moreover, our identified conserved associated genes are found to be a good resource for studying cell differentiation and reprogramming. Lastly, long non-coding RNAs can serve well as associated genes to indicate cell states. We further infer the biological functions of those non-coding associated genes based on their coexpressed protein-coding genes. This study demonstrates that combining statistical modeling with public RNA-seq data can be powerful for improving our understanding of cell identity control.; National Key Research and Development Plan of China [2016YFA0500803]; National High-Tech Research and Development Program of China [2014AA021103]; National Natural Science Foundation of China [31522030, 31271402]; Tsinghua University Initiative Scientific Research Program [2014z21045]; Computing Platform of National Protein Facilities (Tsinghua University); Department of Statistics at UCLA; Hell-man Fellowship from the Hellman Foundation; National Science Foundation [DMS 1557727, DMS 1613338]; NIH/NIGMS [R01GM120507]; SCI(E); ARTICLE; 4; 1657-1672; 45
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/475026]
专题	生命科学学院
推荐引用方式 GB/T 7714	Yang, Yang,Yang, Yu-Cheng T.,Yuan, Jiapei,et al. Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states[J]. NUCLEIC ACIDS RESEARCH,2017.
APA	Yang, Yang,Yang, Yu-Cheng T.,Yuan, Jiapei,Lu, Zhi John,&Li, Jingyi Jessica.(2017).Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states.NUCLEIC ACIDS RESEARCH.
MLA	Yang, Yang,et al."Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states".NUCLEIC ACIDS RESEARCH (2017).