Pathways that show enrichment of genes by MAGENTA analysis.
| Database | Gene Set | Effective Gene Set Size | No. Expected Genes (> 75% cutoff) | No. Observed Genes (> 75% cutoff) | Nominal p | FDR p | Significant Genes* |
|---|---|---|---|---|---|---|---|
| GOTERM | Dorsal/ventral neural tube patterning | 13 | 3 | 11 | 1.00 × 10−5 | 5.60 × 10−3 | PAX7, SHH, GLI2, BMP4, PTCH1, SMO, MNX1, PSEN1, GSC, PSEN2, FOXA2 |
| GOTERM | Iron ion transport | 22 | 6 | 15 | 1.00 × 10−4 | 1.09 × 10−2 | STEAP4, STEAP3, SLC25A28, SLC39A14, SLC40A1, SFXN5, FTL, TTYH1, STEAP2, MFI2, SFXN1, SFXN2, SFXN4, TF, FTH1 |
↵* Enriched genes with scores in the top 25% of all gene scores. Best SNP p values range from 1.68 × 10−3 to 1.27 × 10−6 for the dorsal/ventral neural tube patterning pathway and from 2.62 × 10−3 to 1.18 × 10−4 for the iron ion transport pathway. MAGENTA: Meta-Analysis Gene-set Enrichment of variant Associations; FDR: false discovery rate.