Additional file 1: of The wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in drosophila melanogaster

Table S1. Structural equation modeling measures of overall model fit. Adapted from (Hoyle). Table S2. DSPR no covariance raw residual matrix of genes in the sex hierarchy GRN. Table S3. CEGS no covariance raw residual matrix of genes in the sex hierarchy GRN. Table S4. New links added between genes in the DSPR sex hierarchy GRN. Table S5. New links added between genes in the CEGS sex hierarchy GRN. Table S6. Gene added to the CEGS sex hierarchy GRN. Table S7. Number of alleles per gene of the sex determination hierarchy in a random 50 % subset of CEGS lines. Table S8. Genes added to the sex hierarchy GRN that showed enrichment for chromatin binding and helicase activity. Table S9. DSPR isoform level factor analysis. Table S10. DSPR gene level factor analysis. Table S11. CEGS exonic regions factor analysis. Table S12. CEGS gene level factor analysis. Table S13. DSPR isoform level modulated modularity clustering (MMC). Table S14. CEGS exon level modulated modularity clustering (MMC). Figure S1. Graphical Gaussian network of genes in the sex determination hierarchy (DSPR Collapsed Isoforms). Figure S2. Examples of secondary neighborhood structure from a genome-wide graphical Gaussian network. Figure S3. Distribution of genes in the sex hierarchy. Figure S4. Correlation and covariance matrices for genes in the sex hierarchy. (DOCX 1153 kb)

Additional file 2: of GWASeq: targeted re-sequencing follow up to GWAS

Regional plots of associations for each targeted region. rs numbers and purple circles indicate the focal GWAS SNP that the region was selected around. Colored circles indicate degree of LD among SNPs. Grey circles indicate novel SNPs that lack LD information based on the 2012 release of the 1000 Genomes data. The rs number at figure top is centered around the location of the focal SNP. (ZIP 1921 kb

Additional file 1: of GWASeq: targeted re-sequencing follow up to GWAS

Boxplot of per-sample coverage by region, for each of the sequenced regions, by case–control status. (TIFF 8219 kb