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Department of Biomedicine

Lars Bolund

Genome-wide annotation of protein-coding genes in pig

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

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Genome-wide annotation of protein-coding genes in pig. / Karlsson, Max; Sjöstedt, Evelina; Oksvold, Per et al.
In: BMC Biology, Vol. 20, 25, 01.2022.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

Harvard

Karlsson, M, Sjöstedt, E, Oksvold, P, Sivertsson, Å, Huang, J, Álvez, MB, Arif, M, Li, X, Lin, L, Yu, J, Ma, T, Xu, F, Han, P, Jiang, H, Mardinoglu, A, Zhang, C, von Feilitzen, K, Xu, X, Wang, J, Yang, H, Bolund, L, Zhong, W, Fagerberg, L, Lindskog, C, Pontén, F, Mulder, J, Luo, Y & Uhlen, M 2022, 'Genome-wide annotation of protein-coding genes in pig', BMC Biology, vol. 20, 25. https://doi.org/10.1186/s12915-022-01229-y

APA

Karlsson, M., Sjöstedt, E., Oksvold, P., Sivertsson, Å., Huang, J., Álvez, M. B., Arif, M., Li, X., Lin, L., Yu, J., Ma, T., Xu, F., Han, P., Jiang, H., Mardinoglu, A., Zhang, C., von Feilitzen, K., Xu, X., Wang, J., ... Uhlen, M. (2022). Genome-wide annotation of protein-coding genes in pig. BMC Biology, 20, [25]. https://doi.org/10.1186/s12915-022-01229-y

CBE

Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB, Arif M, Li X, Lin L, Yu J, et al. 2022. Genome-wide annotation of protein-coding genes in pig. BMC Biology. 20:Article 25. https://doi.org/10.1186/s12915-022-01229-y

MLA

Karlsson, Max et al. "Genome-wide annotation of protein-coding genes in pig". BMC Biology. 2022. 20. https://doi.org/10.1186/s12915-022-01229-y

Vancouver

Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB et al. Genome-wide annotation of protein-coding genes in pig. BMC Biology. 2022 Jan;20:25. doi: 10.1186/s12915-022-01229-y

Author

Karlsson, Max ; Sjöstedt, Evelina ; Oksvold, Per et al. / Genome-wide annotation of protein-coding genes in pig. In: BMC Biology. 2022 ; Vol. 20.

Bibtex

@article{97501fd94f2647aca21367a3e23a361e,

title = "Genome-wide annotation of protein-coding genes in pig",

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.",

keywords = "Annotation, Gene expression, Genome-wide, Protein-coding genes, Tissue expression profile, Transcriptome",

author = "Max Karlsson and Evelina Sj{\"o}stedt and Per Oksvold and {\AA}sa Sivertsson and Jinrong Huang and {\'A}lvez, {Mar{\'i}a Bueno} and Muhammad Arif and Xiangyu Li and Lin Lin and Jiaying Yu and Tao Ma and Fengping Xu and Peng Han and Hui Jiang and Adil Mardinoglu and Cheng Zhang and {von Feilitzen}, Kalle and Xun Xu and Jian Wang and Huanming Yang and Lars Bolund and Wen Zhong and Linn Fagerberg and Cecilia Lindskog and Fredrik Pont{\'e}n and Jan Mulder and Yonglun Luo and Mathias Uhlen",

note = "{\textcopyright} 2022. The Author(s).",

year = "2022",

month = jan,

doi = "10.1186/s12915-022-01229-y",

language = "English",

volume = "20",

journal = "B M C Biology",

issn = "1741-7007",

publisher = "BioMed Central Ltd.",

}

RIS

TY - JOUR

T1 - Genome-wide annotation of protein-coding genes in pig

AU - Karlsson, Max

AU - Sjöstedt, Evelina

AU - Oksvold, Per

AU - Sivertsson, Åsa

AU - Huang, Jinrong

AU - Álvez, María Bueno

AU - Arif, Muhammad

AU - Li, Xiangyu

AU - Lin, Lin

AU - Yu, Jiaying

AU - Ma, Tao

AU - Xu, Fengping

AU - Han, Peng

AU - Jiang, Hui

AU - Mardinoglu, Adil

AU - Zhang, Cheng

AU - von Feilitzen, Kalle

AU - Xu, Xun

AU - Wang, Jian

AU - Yang, Huanming

AU - Bolund, Lars

AU - Zhong, Wen

AU - Fagerberg, Linn

AU - Lindskog, Cecilia

AU - Pontén, Fredrik

AU - Mulder, Jan

AU - Luo, Yonglun

AU - Uhlen, Mathias

PY - 2022/1

Y1 - 2022/1

N2 - 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.

AB - 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.

KW - Annotation

KW - Gene expression

KW - Genome-wide

KW - Protein-coding genes

KW - Tissue expression profile

KW - Transcriptome

U2 - 10.1186/s12915-022-01229-y

DO - 10.1186/s12915-022-01229-y

M3 - Journal article

C2 - 35073880

VL - 20

JO - B M C Biology

JF - B M C Biology

SN - 1741-7007

M1 - 25

ER -