Fig. 3

Characterization of RPL5-deficient zebrafish embryos transcriptome and identification of differentially expressed genes. a Transcriptome analysis identified 280 genes specifically expressed in RPL5 MO, 289 genes specifically expressed in Control, and 12916 commonly expressed genes. In the commonly expressed genes, 363 significantly up-regulated genes and 1606 significantly down-regulated genes in the RPL5 MO were detected using Cuffdiff (fold-change > 2 and p-value < 0.05). Venn diagram summarizes the number of differentially expressed genes, shared and distinct genes expressed in RPL5 MO and Control. b Representative experimental validation of the regulated genes by Real-time PCR analysis. Gene expression was represented as mean ± SD and Two-way ANOVA was performed for comparison between Control and RPL5-deficient zebrafish embryos (**P < 0.001, *P < 0.01, n = 3). Gene expression in Control samples was normalized to 1. c-d The expression patterns of up-regulated genes (c) and down-regulated genes (d), which was detected due to RPL5-deficiency, in other zebrafish models were showed by heatmaps. The corresponding GO enrichment analysis for genes in coordinated regulatory trend, genes in opposite regulatory trend, and genes with no regularities compared with other DBA zebrafish models was performed by DAVID tool. e Differentially expressed RP genes were detected in each DBA zebrafish model, which was separately compared with Control to filter the differentially expressed RP genes with threshold of fold-change > 2 and p-value < 0.05. f Network analysis of differential expressed genes based on FunCoup web source. The yellow diamond represents the significantly differential expressed gene in RPL5-deficient zebrafish embryos (FPKM > 1, fold-change > 2, FDR < 0.05). Other nodes are connected with our query genes by 1-expansion-depth. All the lines represent direct correlation of nodes