In vitro and in vivo characterization of <i>Caenorhabditis elegans</i> PHA‐4/FoxA response elements
Bibliographic record
Abstract
Caenorhabditis elegans PHA-4 is a member of the FoxA group of transcription factors. PHA-4 is critical for development of the C. elegans pharynx and directly regulates most or all pharyngeal genes. The consensus binding site of PHA-4 has not been identified, with previous analysis of PHA-4 targets relying on the mammalian FoxA consensus. Here, we use in vitro and in vivo analyses to demonstrate three features of PHA-4 response elements. First, the PHA-4 consensus matches that of other FoxA proteins, but only a subset of possible sites is active in an in vivo assay. Second, sequence flanking the core PHA-4 site can influence the strength of reporter expression in vivo, as seen for other Fox proteins. Third, in the context of some pharyngeal promoters, PHA-4 response elements are flanked by distinct cis-regulatory elements that modulate response to PHA-4, generating gene expression in specific pharyngeal cell types.
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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 | 0.000 |
| 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) | 0.000 | 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".