Table 3.
Dominant enrichment patterns of phenotypic traits affected by offspring survival (OS) genes linked with LTR7 and LTR5_Hs regulatory loci
| Classification category | LTR7 | LTR7 OS genes | LTR7 non-OS genes | LTR5_Hs | LTR5_Hs OS genes | LTR5_Hs non-OS genes |
|---|---|---|---|---|---|---|
| Number of associated genes | 2957 | 562 | 2395 | 935 | 126 | 809 |
| Significantly enriched records of phenotypic traits identified by the GSEA of genomic databases | ||||||
| DisGeNET database | 72 | 1518 | 0 | 1 | 191 | 1 |
| PanglaoDB augmented 2021 | 70 | 67 | 33 | 3 | 4 | 0 |
| CellMarker augmented 2021 | 203 | 181 | 83 | 3 | 0 | 2 |
| Azimuth cell types 2021 | 89 | 17 | 47 | 0 | 0 | 0 |
| ARCHS4 human tissues | 36 | 37 | 24 | 2 | 11 | 0 |
| Human gene atlas | 2 | 10 | 0 | 0 | 1 | 0 |
| Allen brain atlas database of up-regulated genes | 420 | 506 | 43 | 0 | 0 | 0 |
| Allen brain atlas database of down-regulated genes | 101 | 230 | 5 | 0 | 1 | 0 |
| GTEx tissues’ expression database of up-regulated genes | 334 | 583 | 129 | 0 | 48 | 0 |
| GTEx tissues’ expression database of down-regulated genes | 98 | 329 | 56 | 0 | 80 | 0 |
| Reactome 2016 | 3 | 50 | 0 | 2 | 77 | 1 |
| WikiPathway 2021 human | 1 | 68 | 0 | 0 | 20 | 0 |
| KEGG 2021 human | 2 | 38 | 1 | 1 | 15 | 1 |
| BioPlanet 2019 | 6 | 111 | 1 | 3 | 4 | 1 |
| Jensen diseases database | 40 | 75 | 15 | 4 | 6 | 3 |
| MGI mammalian phenotype level 4 2021 | 25 | 1253 | 0 | 0 | 207 | 0 |
| Human phenotype ontology | 3 | 466 | 0 | 0 | 26 | 0 |
| GTEx aging signatures 2021 | 14 | 0 | 11 | 0 | 0 | 0 |
| Disease perturbations from GEO up-regulated genes | 63 | 160 | 14 | 0 | 0 | 0 |
| Disease perturbations from GEO down-regulated genes | 88 | 153 | 23 | 0 | 0 | 0 |
| Significantly enriched records of phenotypic traits identified by the GSEA of human rare diseases databases | ||||||
| Rare diseases GeneRIF gene lists | 1 | 497 | 0 | 0 | 5 | 0 |
| Rare diseases AutoRIF gene lists | 15 | 738 | 0 | 0 | 2 | 0 |
| Rare diseases AutoRIF ARCHS4 predictions | 57 | 161 | 0 | 0 | 0 | 0 |
| Rare diseases GeneRIF ARCHS4 predictions | 47 | 137 | 0 | 0 | 11 | 0 |
| Significantly enriched records of phenotypic traits identified by the GSEA of targeted TF perturbations, TF PPI, and PPI Hub Proteins genomic databases | ||||||
| TF perturbations followed by expression | 368 | 704 | 76 | 4 | 26 | 1 |
| Transcription factor PPIs | 0 | 86 | 0 | 0 | 0 | 0 |
| PPI hub proteins | 0 | 105 | 0 | 0 | 9 | 0 |
Gene Set Enrichment Analyses (GSEA) were carried out for each gene set and numbers of significantly enriched phenotypic traits defined at the adjusted p values < 0.05 were recorded. Complete lists of phenotypic traits, associated genes, and corresponding statistical metrics for analyzed genomic databases are reported in the Supplement
TF transcription factors, PPI protein–protein interactions, GEO gene ontology omnibus