Extended Data Fig. 3: The pig gene expression atlas.

a, Tissue-specific expression of five transcript types reflected by the TAU score. PCG: protein-coding genes. b, Gene numbers (left), expression pattern (middle, transcripts per million, TPM), and enriched Gene Ontology (GO) terms (right) of tissue-specific genes in 34 tissues. c, Enrichment of muscle-specific genes in 15 chromatin states across 14 pig tissues¹⁶. The red dots represent respective chromatin states in muscle. The blue line indicates enrichment fold = 1. d, Expression profiles of MYL2 gene across 34 tissues (left). The tissue color key is the same as in (b). Chromatin state distribution (right) around MYL2 in 14 pig tissues¹⁶. In brief, red is for promoters, yellow for enhancers, blue for open chromatin and gray for repressed regions. e, Enrichment of tissue-specific genes for two active chromatin states across 11 tissues, which have both chromatin states and gene expression data. The dots represent enrichments from matching tissues. TssA is for active TSS (promoter), and EnhA for active enhancers. f, Comparison of genes with and without functional annotation (referred to as ‘annotated genes’ and ‘unannotated genes’, respectively) in gene co-expression modules at different biological layers. The gene co-repression analysis was conducted using five complementary methods, including WGCNA, ICA, PEER, MEGENA and CEMiTool. ‘All’ shows the combined results from the five methods. The functional annotation was based on the Gene Ontology database (version 2022-01-18). The plots from top to bottom include gene counts, expression level, PhastCons score from 100 vertebrate genomes, proportion of orthologous genes in humans and TAU values. Significant differences between annotated and unannotated genes were obtained using a two-sided Student t-test. ** means P < 0.01. g, An example of gene co-expression module in the pituitary, which includes 59 unannotated and 42 annotated genes, respectively. The functional annotated genes are significantly (P = 8 × 10⁻³) enriched in neuron apoptotic processes. The gray edges between genes represent Pearson’s correlations of expression across all 53 samples in the pituitary. h, The proportion of unannotated genes in each gene co-expression modules across 34 tissues.