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Fig. 1 | Genome Biology

Fig. 1

From: Enteric infection induces Lark-mediated intron retention at the 5′ end of Drosophila genes

Fig. 1

Enteric infection leads to extensive changes in transcript isoform ratios and to greater isoform diversity. a Top: schematic illustrating how genes with different isoform ratios are compared between two conditions. MISO [16] was used to calculate the ratios of different annotated isoforms, and thereafter, the rasp package [15] was used to determine significance (p-homogeneity > 0.05, BH adjusted p value < 0.05, effect size > 0.1). Bottom: Venn diagram of the number of expressed genes whose isoform ratios were significantly altered after infection. b Graphical representation of enriched biological process gene ontology terms based on the list of genes whose isoform ratios were altered after infection. The GO analysis was performed using the GOstats R package [18] (Hypergeometric test p value < 0.005), and REVIGO [19] was used to reduce redundancy in the ontology groups and plot them by semantic similarity (allowed similarity = 0.7). The size of each circle indicates the number of genes belonging to a certain GO category, and the color indicates enrichment significance. c The distribution of Shannon entropies of transcript ratios of each gene per DGRP gut transcriptome. Uninfected (control) and P.e.-infected samples are depicted in gray and brown, respectively. The densities were obtained using R’s base density function. d Breakdown of average Shannon entropy per sample by isoform number, susceptibility class, and treatment condition

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