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Fig. 4 | BMC Genomics

Fig. 4

From: Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data

Fig. 4

(a) Classification of predicted Iso-seq genes into known, novel-intergenic and novel-intragenic genes using Ensembl (release93) and NCBI (release 109) Sscrofa11.1 annotations by UpSetR [65]. Proportion of protein-coding genes in each class is identified by “orange” color. Intersections related to annotated genes are identified by “green” lines. (b) Distribution of transcripts across different classes of predicted genes. (c) Comparison of predicted and annotated genes in term of average number of produced transcripts. Number of genes in each class is shown on each bar. (d) Proportion of transcripts produced by novel and known genes in different transcript biotypes. (e) Gene biotypes. (f) Classification of genes into spliced and un-spliced genes using UpSetR [65]. (g) Classification of novel genes based on the number of tissues in which they were detected. (h) Validation of novel-intergenic genes detected in liver tissue by an independent liver chromatin immunoprecipitation (ChIP) sequencing experiment (2 histone modifications per sample). Venn diagram shows the distribution of 616 validated genes (with significant H3K4m3e and H3K36me3 peaks) across samples. (i) validation of NCBI specific Iso-seq genes that were located in intergenic region of pig genome based on Ensembl gene set (see text) detected in liver tissue by an independent liver ChIP sequencing experiment (2 histone modifications per sample). Venn diagram shows the distribution of 358 validate genes (with significant H3K4m3e and H3K36me3 peaks) across samples. (j) validation of liver detected Ensembl specific Iso-seq genes that were located in intergenic region of pig genome based on Ensembl gene set (see text) by an independent liver ChIP sequencing experiment (2 histone modifications per sample). Venn diagram shows the distribution of 137 validate genes (with significant H3K4m3e and H3K36me3 peaks) across samples

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