Fig. 2

Bubble charts of enriched biological processes in RPE cell cultures and comparison with in vivo obtained sample data. A Enriched biological processes identified from genes significantly associated with time in culture. Each process is represented by a bubble on the Y-axis. Bubble size reflects the number of SCGs annotated to the corresponding GO term, while color indicates the significance of enrichment (q value). The X-axis shows the enrichment ratio (number of SCGs annotated to the GO term divided by the total number of genes annotated to that GO term). B Top 20 most significantly enriched biological processes raised by DEGs between 25 (n = 2) and 4 weeks (n = 3) in culture. C Venn diagram showing overlap of time-associated genes in RPE cell cultures with genes from ageing dataset (Ref. GSE159435) and dry AMD dataset (Ref. 10.5281/zenodo.7020215). D Genes exhibiting similar expression patterns over time when comparing RPE cell cultures and donor age (“Ageing” dataset). E Genes showing similar expression trends over time in RPE cell cultures and AMD diagnosed patients (“AMD” dataset). Where applicable, the analyses included data from three biological replicates of cell cultures at 4, 12, and 17 weeks, along with two additional replicates at 25 weeks. Additionally, the dataset comprised 13 replicates of RPE samples from the “AMD” dataset and 85 replicates of macular RPE/choroid from “Ageing” dataset