Additional file 1 of Increased CpG methylation at the CDH1 locus in inflamed ileal mucosa of patients with Crohn disease
Bibliographic record
Abstract
Additional file 1. Fig. S1. Scheme of the genomic map (5’) proximal from the CDH1 gene. Studied CpGs are figured as CGI, or as lollipops for the 1st enhancer. The rs16260 A/C variant is shown. Fig. S2. ROC curve testing the association between CD and the methylation at the CDH1 locus in ileal mucosa. A logistic regression explored the association between CD and the enhancer CpGs according to the methylation status of CGI. The coefficient of the latter adjustment variable was used to weigh the enhancer CpGs value based on the CGI methylation status. Fig. S3. Correlation of the methylation of the 1st enhancer studied CpGs in the mucosa of pooled CD and control patients. R (p value). Fig. S4: Correlation of the methylation of the 1st enhancer studied CpGs in PBMC of pooled CD and control patients. R (p-value). Fig. S5. Methylation of the 1st enhancer CpGs in (A) mucosa; (B) PBMC of patients with CD or controls, according to the methylation status of the CGI. No significant differences were detected. Table S1. Complete individual methylation data in the studied CD patients and controls. Table S2. Methylation in mucosa does not depend on rs16260 (C>A) genotype. However, we observed non-significant trend for increased CGI methylation in patients with CC genotype. No had AA genotype was present. Mean (±SD); decimal values rounded to the nearest integer.
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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 | 0.027 |
| Meta-epidemiology (narrow) | 0.001 | 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) | 0.865 | 0.098 |
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".