Fig. 3: PLS-DA and volcano plots of each IRD subgroup compared with that of the control group.

The significant features highlighted in the volcano plot were defined as having a false discovery rate <0.05 (Benjamini–Hochberg test, two-sided) and fold change >2. The number of metabolite features with significant differences between each IRD subgroup and control group was shown in the parentheses in each volcano plot. No metabolite feature could be identified between the BCD and control group (g). The PLS-DA plot showed that the RP, CD/CRD, and STGD groups could be distinguished from the control group in metabolomic analysis (a, c, e), while the overlapping area in the BCD group was more prominent (g). Moreover, when we further sub-grouped RP by genotype, including EYS, USH2A, ABCA4, and PRPF31, the metabolomic analysis showed more distinguishable results in the PLS-DA plot (b, d, f, h). i Compared between CD/CRD and STGD, 71 features could be identified with significant differences from the volcano plots, and the two groups could be distinguished in the PLS-DA plot. j Compared with RP with the ABCA genotype, STGD showed that only 19 features in the volcano plots could be identified, and the overlapping of the PLS-DA plot was prominent. Despite the significant phenotypic differences, RP and STGD with the same genotype, ABCA4, showed similar metabolomic profiles. Source data are provided as a Source Data file. IRD, inherited retinal degeneration, BCD, Bietti’s crystalline dystrophy, CRD, cone-rod dystrophy, RP, retinitis pigmentosa; STGD, Stargardt disease, PLS-DA, partial least squares-discriminant analysis.