Fig. 2

Categorization of genes that are differentially expressed in photoreceptor-directed fibroblasts derived from an EYS-RP patient and upregulated by transduction of CRX, RAX, NeuroD and OTX2. Venn diagrams (A, B) and Mean-average (MA) plots (C, D) to compare EYS-RP cells vs normal cells. To clarify the specific gene expression profile in induced photoreceptor cells derived from EYS-RP patients, we compared the expression profiles of 58,201 probes in the induced photoreceptor cells or non-induced fibroblast cells derived from an EYS-RP patient (induced or non-induced, RP, Pt#1) and healthy volunteers (induced or non-induced, normal, N#3), using microarrays. We first extracted the intersection of the two groups of genes, i.e., up- or downregulated genes in RP versus healthy ([induced Pt#1] versus [induced N#3], which is an age-matched pair for comparison) (signal ratio ≥  + 1.5, ≤ -1.5 for “up,” “down”) and those in CRNO-transduced normal fibroblasts versus non-induced fibroblasts ([induced N#3] versus [non-induced N#3]) (signal ratio ≥  + 1.5) (A). Furthermore, we compared non-induced EYS-RP-derived cells and non-induced normal cells, and then extracted the intersection of the two groups to define up- or downregulated genes (non-induced Pt#1] versus [non-induced N#3]). We also determined up- or downregulated genes in induced RP versus induced healthy ([induced Pt#1] versus [induced N#3]) (signal ratio ≥  + 1.5, ≤ -1.5) (B). Mean-average (MA) plots indicate differential gene expression between induced RP and induced normal (C) and differential gene expression between non-induced RP and non-induced normal (D). Significantly differentially upregulated genes (signal ratio ≥  + 1.5) are highlighted in red and downregulated genes (signal ratio ≤ -1.5) are highlighted in n green