Fig 1.
Variable gene expression patterns in retina and choroid during myopia progression.
The clustered patterns of variable gene expression during the day are shown for the retina: occluded eyes (A) and contralateral open eyes (B); and for the choroid: occluded eyes (C) and contralateral open eyes (D). Subsets of the varying genes generated these expression patterns using statistical criteria described in the text, with the number of varying genes used to form each group above each panel. The densities of the tracings in each group reflect the number of genes conforming to each specific cluster. To illustrate the light:dark transitions, the bottom bars on each panel indicate the light phase (white bar) beginning at ZT0, and the dark phase (black bar) beginning at ZT12 and ending at ZT0. See S2A–S2D Table for the variability data of all genes over time for each tissue and eye, ranked by p-adj values. Abscissa: times of tissue sampling in ZT (hours). Ordinate or Z-scores: 0 = mean, with non-zero values corresponding to ± S.D.
Fig 2.
Gene expression patterns for the OcclVopen*time interactions during myopia progression, for retina and choroid.
The groups into which genes clustered for the OcclVopen*time interactions over one day are shown for retina (A) and choroid (B). The limited number of genes meeting the criteria of p-adj<0.05 or p-adj<0.1 necessitated applying weaker statistical criteria to generate these groupings (see Results text). Most but not all interacting genes showed expression patterns demonstrated by these identified groups. The number of genes assignable to the individual groups appear above each panel. To illustrate light:dark transitions, the bottom bars on each panel signify the light phase (white bar) beginning at ZT0, and the dark phase (black bar) beginning at ZT12 and ending at ZT0. See S4A and S4B Table for the complete list of genes in each tissue in the occlVopen*time interaction category, including group assignment, gene names and descriptions, ranked by p-adj values. S1A Fig (retina) and S1B Fig (choroid) show heatmaps for the individual genes in the occlVopen*time interactions category meeting the p-adj<0.01 criterion. Abscissa: times of tissue sampling in ZT (hours). Ordinate or Z-scores: 0 = mean, with non-zero values corresponding ± S.D.
Table 1.
Number of genes with varying expression levels over time.
Table 2.
Number of genes with occluded vs. open eye expression differences at each time, myopia progression.
Table 3.
Overall category, retina, genes with similar differences over the day during myopia progression.
Table 4.
Genes with occlVopen*time interactions during myopia progression.
Fig 3.
Venn diagrams: Genes with occluded vs. open eye differences at the sampling times during myopia progression, retina and choroid.
The Venn diagrams identify the number of genes with differential expression levels at more than one time comparing occluded vs. open eyes in retina and in choroid, with the criterion of p-adj<0.05 for occluded vs. open eyes (see S3A and S3B Table). The different shapes of the Venn diagrams in the two panels occurred because the number of times with differentially expressed genes (Table 2) differed between retina (5 times) and choroid (4 times). S5 Table indicates times, the number of genes differentially expressed at the indicated times, the specific genes altered at more than one time, the directions of gene expression change and the log2 fold changes for both tissues.
Table 5.
Genes with occluded vs. open eye differences at more than one time during myopia progression.
Table 6.
Common genes from occluded vs. open chick eyes and candidate human myopia genes.