Figure 4 | Scientific Reports

Figure 4

From: Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations

Figure 4

Functional analysis and validation of the high confident exon skipping events discovered across lens developmental states. (a) Functional enrichment analysis of genes associated with high confidence (FDR 1%) skipped exon events identified using rMATS27 pipeline in atleast one pairwise comparison of developmental stages. For each biological process per group (color coded), the % genes per GO term with number of query genes (** in red) in the analysis is shown in histogram. This shows the functional grouping of the GO-terms based on GO hierarchy using the Cytoscape67-ClueGO31 plugin. Significant clusters (p < 1e-2), color coded by group based on enriched GO-biological processes generated from ClueGO analysis with size of the nodes indicating level of significant association of genes per GO-term. (b) Experimental validation by RT-PCR analysis of a selected set of high confident skipped exonic events reveals that selected mRNA isoforms with skipped events are more abundant during embryonic and perinatal stages. The schematic of the expected products are shown next to the gene. For validation, primers (arrows) were designed on the exons (black box) flanking the alternatively spliced exon (grey box). For all the genes, band with higher molecular weight is the isoform including the alternatively spliced exon and band with lower molecular weight is the isoform with the skipped exon. Hprt represents a loading control. Negative control is included for all isoforms tested where the RT-PCR reaction was performed using the same primers as for the isoforms but without any cDNA. Full-length gels are included in Fig. S6.