Figure 4.
Figure 4. Functional analysis of differentially translated genes demonstrates enrichment for DNA repair pathways. The 748 genes that are differentially translated between type A and type B were subjected to a function and pathway enrichment analysis using (1) QIAGEN's Ingenuity Pathway Analysis tool (IPA, https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/), (2) Biological Process GO terms attached to the genes using the DAVID Functional Annotation tool, and (3) GSEA. Eighty-eight genes were extracted from this analysis; of which, 16 are found in IPA's DNA repair-related canonical pathways (adjusted P < .001), are enriched in IPA DNA repair-related functional groupings (adjusted P < .001), and are annotated by DAVID with DNA repair relevant GO terms (FDR < 0.001). Forty-one are found by 2 of these methods and the remainder by 1 method. The Ingenuity canonical pathways are: DNA Double-Strand Break Repair by Homologous Recombination, DNA Double-Strand Break Repair by Non-Homologous End Joining, Role of BRCA1 in DNA Damage Response, and ATM Signaling. The Ingenuity functions are: DNA damage response of cells, double-stranded DNA break repair, double-stranded DNA break repair of cells, and repair of DNA. The DAVID terms are: GO:0006974 (cellular response to DNA damage stimulus) and GO:0006281 (DNA repair). The GSEA results confirm an enrichment of genes involved in the ATM signalling pathway. The right column presents the fold change in translational efficiency of cluster A as compared to cluster B. Twelve genes are downregulated in cluster A, but all other genes are upregulated. Genes in the ATM pathway. either upstream (ie, MRE11, RAD50, and NBN) or interacting (ie, RBBP8, RAD17, and RIF1), are highlighted (blue). Apart from RIF1 all of these genes are present in all 4 of the analyses.

Functional analysis of differentially translated genes demonstrates enrichment for DNA repair pathways. The 748 genes that are differentially translated between type A and type B were subjected to a function and pathway enrichment analysis using (1) QIAGEN's Ingenuity Pathway Analysis tool (IPA, https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/), (2) Biological Process GO terms attached to the genes using the DAVID Functional Annotation tool, and (3) GSEA. Eighty-eight genes were extracted from this analysis; of which, 16 are found in IPA's DNA repair-related canonical pathways (adjusted P < .001), are enriched in IPA DNA repair-related functional groupings (adjusted P < .001), and are annotated by DAVID with DNA repair relevant GO terms (FDR < 0.001). Forty-one are found by 2 of these methods and the remainder by 1 method. The Ingenuity canonical pathways are: DNA Double-Strand Break Repair by Homologous Recombination, DNA Double-Strand Break Repair by Non-Homologous End Joining, Role of BRCA1 in DNA Damage Response, and ATM Signaling. The Ingenuity functions are: DNA damage response of cells, double-stranded DNA break repair, double-stranded DNA break repair of cells, and repair of DNA. The DAVID terms are: GO:0006974 (cellular response to DNA damage stimulus) and GO:0006281 (DNA repair). The GSEA results confirm an enrichment of genes involved in the ATM signalling pathway. The right column presents the fold change in translational efficiency of cluster A as compared to cluster B. Twelve genes are downregulated in cluster A, but all other genes are upregulated. Genes in the ATM pathway. either upstream (ie, MRE11, RAD50, and NBN) or interacting (ie, RBBP8, RAD17, and RIF1), are highlighted (blue). Apart from RIF1 all of these genes are present in all 4 of the analyses.

Close Modal

or Create an Account

Close Modal
Close Modal