Additional file 1 of Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
Bibliographic record
Abstract
Additional file 1: Fig. S1. Stepwise epigenetic modification of cytosine. Fig. S2. Relationship between unmodified versus modified motif statistical significance of central enrichment (from CentriMo [53]) and modified base calling thresholds across different whole genome bisulfite sequencing (WGBS) and oxidative WGBS (oxWGBS) specimens, in mice [48]. Fig. S3. Relationship between unmodified versus modified ZFP57 statistical significance of central enrichment (from CentriMo [53]) and modified base calling thresholds across different WGBS and oxWGBS specimens, in mice [48]. Fig. S4. Relationship between unmodified versus modified C/EBPβ statistical significance of central enrichment (from CentriMo [53]) and modified base calling thresholds across different WGBS and oxWGBS specimens, in mice [48]. Fig. S5. ZFP57 (Strogantsev et al. [20] CB9; 56 142 ChIP-seq peaks) CentriMo analysis of de novo and JASPAR motifs (Methods). Fig. S6. CentriMo [53] results for OCT4 cleavage under targets and release using nuclease (CUT&RUN) in mouse embryonic stem cells (mESCs). Fig. S7. Modified versus unmodified motifs, combining score and cluster information, for a wide array of transcription factors.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.891 | 0.000 |
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 teacher head, 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".