Additional file 2 of DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits
Bibliographic record
Abstract
Additional file 2: Supplementary Figure S1. Correlation between gene expression and methylation levels of different genetic regions at a scale of the whole genome. Supplementary Figure S2. Comparison of the global methylation levels of different genetic regions between SAP and HC group. Supplementary Figure S3. Comparison of the global methylation levels of CpG islands (CGI), shores and shelves between SAP and HC groups. Supplementary Figure S4. Comparison of global methylation level of cytosines in the context of CHG and CHH between SAP and HC group. Supplementary Figure S5. Comparison of global methylation level of cytosines in the context of CHG located in CpG islands (CGI), shores and shelves between SAP and HC groups. Supplementary Figure S6. Density of CpG sites in LINE-1 and t-RNA-derived SINEs. Supplementary Figure S7. Summary of identified methylation haplotype blocks (MHBs). Supplementary Figure S8. Identification of differential genes with significant changes in their gene expression level and the general methylation level of first exon (A) and first intron (B). Supplementary Figure S9. de novo identified motifs in GE-dMHBs. Supplementary Figure S10. Boxplots showing the methylation difference of select GE-dMHBs between cows with high or low milk somatic cell count (SCC). Supplementary Figure S11. Boxplots showing the methylation difference of selected GE-dMHBs between cows with high or low milk yield (MY).
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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 | 0.019 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.843 | 0.114 |
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".