nhr-119
C. elegans
Nuclear Hormone Receptor family
What the model saw
Gene: nhr-119 Organism: Caenorhabditis elegans Known functions: Nuclear Hormone Receptor family. DNA-binding transcription factor activity. RNA polymerase II cis-regulatory region sequence-specific DNA binding. sequence-specific DNA binding. zinc ion binding.
View unredacted entry
Nuclear Hormone Receptor family. DNA-binding transcription factor activity. RNA polymerase II cis-regulatory region sequence-specific DNA binding. sequence-specific DNA binding. zinc ion binding.
Solver output
nhr-119 is a member of the C. elegans Nuclear Hormone Receptor (NHR) superfamily, which includes transcription factors that regulate metabolism, development, and stress responses via ligand-dependent DNA binding. NHRs in C. elegans are broadly linked to nutrient sensing and metabolic regulation, analogous to mammalian nuclear receptors like PPARs and LXRs. However, the NHR family in C. elegans is massively expanded (~284 members), and without specific ligand identity, target gene information, or functional studies for nhr-119 specifically, it is not possible to determine whether its transcriptional program promotes or opposes longevity. Its zinc-finger DNA-binding and RNA Pol II cis-regulatory binding activities confirm it is a bona fide transcription factor, but the direction of its effect on aging pathways (e.g., DAF-16/FOXO, NHR-49/PPARα, or others) cannot be inferred from these annotations alone.
GenAge curators classify each gene's normal function as promoting (Pro-Longevity) or opposing (Anti-Longevity) longevity, based on synthesis across studies. Loss-of-function effects can vary from this depending on the manipulation.
Advisor judgment
The model predicted "unclear" while the ground truth is "pro_longevity." The model's reasoning is sound given the limited information provided - it correctly identifies nhr-119 as part of the massively expanded NHR family in C. elegans and acknowledges that without specific functional studies, the direction of effect cannot be determined. The model appropriately hedged given the sparse annotation, but ultimately got the answer wrong. The mechanism class of "deregulated_nutrient_sensing" is a reasonable guess for an NHR family member but cannot be confirmed as correct. The confidence of 0.35 reflects appropriate uncertainty. This is a case where the model was appropriately uncertain rather than confidently wrong, but the answer is still incorrect.
Raw API responses
solver
{
"reasoning": "nhr-119 is a member of the C. elegans Nuclear Hormone Receptor (NHR) superfamily, which includes transcription factors that regulate metabolism, development, and stress responses via ligand-dependent DNA binding. NHRs in C. elegans are broadly linked to nutrient sensing and metabolic regulation, analogous to mammalian nuclear receptors like PPARs and LXRs. However, the NHR family in C. elegans is massively expanded (~284 members), and without specific ligand identity, target gene information, or functional studies for nhr-119 specifically, it is not possible to determine whether its transcriptional program promotes or opposes longevity. Its zinc-finger DNA-binding and RNA Pol II cis-regulatory binding activities confirm it is a bona fide transcription factor, but the direction of its effect on aging pathways (e.g., DAF-16/FOXO, NHR-49/PPARα, or others) cannot be inferred from these annotations alone.",
"confidence": 0.35,
"key_pathways": [
"Nuclear hormone receptor signaling",
"RNA polymerase II transcriptional regulation",
"Zinc-finger transcription factor activity"
],
"mechanism_class": "deregulated_nutrient_sensing",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"pro_longevity.\" The model's reasoning is sound given the limited information provided - it correctly identifies nhr-119 as part of the massively expanded NHR family in C. elegans and acknowledges that without specific functional studies, the direction of effect cannot be determined. The model appropriately hedged given the sparse annotation, but ultimately got the answer wrong. The mechanism class of \"deregulated_nutrient_sensing\" is a reasonable guess for an NHR family member but cannot be confirmed as correct. The confidence of 0.35 reflects appropriate uncertainty. This is a case where the model was appropriately uncertain rather than confidently wrong, but the answer is still incorrect.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}