Additional file 2 of Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice
Bibliographic record
Abstract
Additional file 2: Table S7. Genes located in low nucleotide diversity regions (top 5%) in classical inbred mice strains as compared to wild and wild-derived inbred mice. Table S8. Functional categories of the genes (p < 0.05) located at low nucleotide diversity regions (top 5%) in classical inbred mice strains as compared to wild and wild-derived inbred mice. Table S9. Genes located in top 5% Fst regions in classical inbred mice strains as compared to wild and wild-derived inbred mice. Table S10. Functional categories of the genes (p < 0.05) located in top 5% Fst regions in classical inbred mice strains compared to wild and wild-derived inbred mice. Table S11. Genes with top 5% XP-CLR score in classical inbred mice strains as compared to wild and wild-derived inbred mice. Table S12. Functional categories of the genes (p < 0.05) with top 5% XP-CLR score in classical inbred mice strains as compared to wild and wild-derived inbred mice. Table S13. Common 339 positively selected genes (PSGs) in classical inbred mice strains as compared to wild and wild-derived inbred mice. Table S14. Functional categories of the common 339 positively selected genes in classical inbred mice strains as compared to wild and wild-derived inbred mice. Table S15. Common 355 positively selected genes between classical inbred mice strains and wild mice after excluding wild-derived inbred mice. Table S16. Genes significantly higher expressed in immature brain/brain than in other tissues. Table S17. Abnormal phenotypes of the 245 genes from 339 PSGs reported in mouse models. Table S18. Differently expressed genes of the 339 PSGs in the hippocampus between classical inbred and wild mice. Table S19. Differently expressed genes of the 339 PSGs in the frontal lobe between classical inbred and wild mice. Table S20. Differently expressed genes of the 339 PSGs in the hypothalamus between classical inbred and wild mice. Table S22. Selected sites with reference allele homozygous not existing in any wild mice, but existing in all the classical inbred mice. Table S24. SNPs located in Astn2 gene with no homozygous of reference allele in wild mice. Table S25. SNPs located in Astn2 gene with high selective potential.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.009 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.707 | 0.123 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".