Amstutz et al., 2022
Cluster-Based Analysis of Retinitis Pigmentosa Modifiers Using Drosophila Eye Size and Gene Expression Data
[10.3390/genes13020386][FBrf0252765]

Description

Computational study without new phenotyping: the F1 eye sizes of DGRP lines crossed to the GMR>Rh1^G69D retinitis pigmentosa model (Chow et al. 2016, study 150) were correlated with gene expression within K-means clusters of 171 lines, giving 10 candidate modifier genes.

Comments from curator

No phenotype data: this study was rejected because no new phenotype was measured on DGRP lines.

This is a computational study. Its only per-line DGRP phenotype is the eye size of the Rh1^G69D model of retinitis pigmentosa in 173 DGRP backgrounds, published by Chow et al. 2016, Human Molecular Genetics 25(4):651-659 (Supplementary Table S1, PMC version). The measured flies are the F1 females of crosses between virgin females of a donor strain carrying GMR-GAL4 and UAS-Rh1^G69D and males of each DGRP line; the area of the left eye of at least 10 females per cross was measured in pixels with ImageJ. The authors used the per-line mean eye sizes of these data (173 lines, from 14,254.6 to 27,349.11 pixels; the first 14 lines are shown in Table 1 of the paper). Chow et al. 2016 is now DGRPool study 150 (added on 2026-11-10), where these eye sizes are stored. The same eye sizes are also reused by DGRPool study 112 (Palu et al. 2020), rejected for the same reason.

What this paper does with them: the 171 lines that have both eye sizes and adult female whole-fly expression data (expression arrays of Huang et al. 2015, ArrayExpress E-MTAB-3216; line 513 was dropped because one of its two expression replicates is missing) were grouped by K-means clustering (6 clusters) on the expression of 18,140 genes. In the two clusters enriched in large-eye (Cluster 1, 38 lines) and small-eye (Cluster 3, 37 lines) strains, the mean eye size was correlated with the expression of each gene (Pearson, Kendall and Spearman), which gave 89 genes and 10 candidate modifiers (Table 3). The R code is on GitHub (code and plots only, no data file).

The validation experiment (RNAi knock-down of 7 candidate genes in the GMR>Rh1^G69D model, eye area of 10-15 females per RNAi strain, Figure 12) was not done in DGRP backgrounds and is not included. There is therefore nothing to upload to DGRPool for this study.

Other external data available

E-MTAB-3216 whole-fly expression arrays of adult females and males of DGRP lines (Huang et al. 2015), female data reused in this study (not generated by it)

DGRP lines

None

Datasets