Genome-wide annotation of protein-coding genes in pig
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Published:2022-01-25
Issue:1
Volume:20
Page:
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ISSN:1741-7007
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Container-title:BMC Biology
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language:en
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Short-container-title:BMC Biol
Author:
Karlsson Max, Sjöstedt Evelina, Oksvold Per, Sivertsson Åsa, Huang Jinrong, Álvez María Bueno, Arif Muhammad, Li Xiangyu, Lin Lin, Yu Jiaying, Ma Tao, Xu Fengping, Han Peng, Jiang Hui, Mardinoglu Adil, Zhang Cheng, von Feilitzen Kalle, Xu Xun, Wang Jian, Yang Huanming, Bolund Lars, Zhong Wen, Fagerberg Linn, Lindskog Cecilia, Pontén Fredrik, Mulder Jan, Luo Yonglun, Uhlen MathiasORCID
Abstract
Abstract
Background
There is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here, a new annotation strategy is introduced based on dimensionality reduction and density-based clustering of whole-body co-expression patterns. This strategy has been used to explore the gene expression landscape in pig, and we present a whole-body map of all protein-coding genes in all major pig tissues and organs.
Results
An open-access pig expression map (www.rnaatlas.org) is presented based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups. A new UMAP-based classification scheme is introduced, in which all protein-coding genes are stratified into tissue expression clusters based on body-wide expression profiles. The distribution and tissue specificity of all 22,342 protein-coding pig genes are presented.
Conclusions
Here, we present a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering. A genome-wide resource of the transcriptome map across all major tissues and organs in pig is presented, and the data is available as an open-access resource (www.rnaatlas.org), including a comparison to the expression of human orthologs.
Funder
knut och alice wallenbergs stiftelse familjen erling-perssons stiftelse sanming project of medicine in shenzhen dff sapere aude starting grant
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Developmental Biology,Plant Science,General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Physiology,Ecology, Evolution, Behavior and Systematics,Structural Biology,Biotechnology
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