Journal
BMC BIOLOGY
Volume 20, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s12915-022-01229-y
Keywords
Annotation; Protein coding genes; Genome wide; Transcriptome; Gene expression; Tissue expression profile
Categories
Funding
- Knut and Alice Wallenberg Foundation (WCPR)
- Erling Persson Foundation (KCAP)
- Sanming Project of Medicine in Shenzhen [SZSM201612074]
- DFF Sapere Aude Starting grant [8048-00072A]
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This study introduces a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering, and presents a whole-body map of protein-coding genes in the pig. The study provides insights into the expression patterns of these genes across different tissues and organs.
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.
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