Genome-wide annotation of protein-coding genes in pig

BMC Biol. 2022 Jan 25;20(1):25. doi: 10.1186/s12915-022-01229-y.


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 ( ) 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 ( ), including a comparison to the expression of human orthologs.

Keywords: Annotation; Gene expression; Genome-wide; Protein-coding genes; Tissue expression profile; Transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Gene Expression Profiling
  • Genome*
  • Genomics*
  • Mammals
  • Molecular Sequence Annotation
  • Organ Specificity
  • Swine / genetics
  • Transcriptome