Comments from curator
No phenotype data: this study was rejected because no phenotype was measured on DGRP lines.This is a computational study (
paper;
PMC version). The authors reanalysed the SNP-level summary statistics of two published longevity GWAS, using Hi-C interaction frequencies (co-location in the nucleus) to build networks between the genomic regions that harbour the associated SNPs:
- DGRP GWAS: the p-values of 2,193,745 SNPs for virgin female lifespan of 197 DGRP lines (Freeze 2.0, about 25 females per line), provided by the authors of Ivanov et al., 2015. These lifespan data are already in DGRPool study 18.
- Synthetic GWAS: the SNP allele frequencies of young females and of the last surviving ~2% of females in two synthetic recombinant populations, each derived from eight inbred founder lines that are not DGRP lines (Burke et al., 2014).
The Hi-C data are those of
Sexton et al., 2012 (GEO
GSM849422). Candidate genes were then prioritised with network measures, community detection, GO enrichment and FlyBase phenotype annotations.
No new phenotype was measured, and the paper reports no value per DGRP line. The tables of the paper and the
Supplementary Tables 1-10 list only genes, SNP counts, network nodes (80 kb or 10 kb genomic bins), clusters, GO enrichments and TAD border analyses. There is therefore nothing to upload to DGRPool.
