Genome-wide annotation of protein-coding genes in pig

被引：19

作者：

Karlsson, Max ^{[1
]}

Sjostedt, Evelina ^{[2
,3
]}

Oksvold, Per ^{[1
]}

Sivertsson, Asa ^{[1
]}

Huang, Jinrong ^{[4
,5
,6
]}

Alvez, Maria Bueno ^{[1
]}

Arif, Muhammad ^{[1
]}

Li, Xiangyu ^{[1
]}

Lin, Lin ^{[6
,7
]}

Yu, Jiaying ^{[4
,5
]}

Ma, Tao ^{[8
]}

Xu, Fengping ^{[4
,5
]}

Han, Peng ^{[5
]}

Jiang, Hui ^{[8
]}

Mardinoglu, Adil ^{[1
]}

Zhang, Cheng ^{[1
]}

von Feilitzen, Kalle ^{[1
]}

Xu, Xun ^{[4
]}

Wang, Jian ^{[4
]}

Yang, Huanming ^{[4
]}

Bolund, Lars ^{[4
,5
,6
]}

Zhong, Wen ^{[1
]}

Fagerberg, Linn ^{[1
]}

Lindskog, Cecilia ^{[3
]}

Ponten, Fredrik ^{[3
]}

Mulder, Jan ^{[2
]}

Luo, Yonglun ^{[4
,5
,6
,7
]}

Uhlen, Mathias ^{[1
,2
]}

机构：

[1] KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden

[2] Karolinska Inst, Dept Neurosci, Stockholm, Sweden

[3] Uppsala Univ, Dept Immunol Genet & Pathol, Uppsala, Sweden

[4] BGI Shenzhen, Shenzhen, Peoples R China

[5] BGI Qingdao, Qingdao Europe Adv Inst Life Sci, Lars Bolund Inst Regenerat Med, Qingdao, Peoples R China

[6] Aarhus Univ, Dept Biomed, Aarhus, Denmark

[7] Aarhus Univ Hosp, Steno Diabet Ctr Aarhus, Aarhus, Denmark

[8] BGI Shenzhen, MGI, Shenzhen, Peoples R China

来源：

BMC BIOLOGY | 2022年 / 20卷 / 01期

关键词：

Annotation; Protein coding genes; Genome wide; Transcriptome; Gene expression; Tissue expression profile; EXPRESSION; MODEL; IMMUNOLOGY; ANTIBODIES; DISCOVERY; FEATURES; RECEPTOR; MINIPIG; ATLAS;

D O I：

10.1186/s12915-022-01229-y

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：18

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