Sequencing analysis
Resolve the dose dependence of AP-1 transcription
Read the task instructions and deliverables
# Resolve the dose dependence of AP-1 transcription WM239A melanoma cells were exposed to DMSO or four doses of trametinib for one hour. The PRO-seq reads measure RNA being made. How does the makeup and total RNA signal of core AP-1 depend on dose, and how much of the observed variation lies between conditions rather than between replicates? Use all ten libraries and the supplied sample records and references. Core AP-1 here means the seven protein-coding Fos and Jun family members. The measurement scale is gene-span RNA read density relative to the summed density of all annotated nuclear protein-coding gene entries. Condition profiles give the two libraries equal weight; the treatment-average profile gives the four treated doses equal weight. AP-1 composition is each member's share of its condition's summed AP-1 profile. Report relative signals at one hour, using the final quantities defined in the submission form. Return only findings.json.
How was it graded?
Code compares submitted answer fields with reference values. Written reasoning is not graded.
Fraction of criteria passed; every criterion has weight one.
LLM judge: None — deterministic grading
Task files
Choose an evidence file.
Grading criteria
Gene symbols for every AP-1 member that has the largest absolute change in AP-1 composition at any individual treated dose compared with vehicle
Earns credit
The composition_drivers field equals ['FOSL1', 'JUND'] after supported identifier normalization.
Does not earn credit
The field is missing, null, invalid, or fails the shared deterministic comparison.
Accepted alternatives
Order does not affect the set comparison. Repeated members, including aliases of the same member, fail the check. Leading and trailing whitespace is ignored. Accepted aliases: ENSG00000175592.9 → FOSL1; ENSG00000175592 → FOSL1; fosl1 → FOSL1; ENSG00000130522.6 → JUND; ENSG00000130522 → JUND; jund → JUND.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.composition_drivers; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.composition_drivers; q20.composition_drivers
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Passed. composition_drivers: matched 2 of 2 reference members. No missing or extra members.
Equal-dose mean distance between treated and vehicle AP-1 compositions, in percentage points
Earns credit
In the submitted JSON, mean_composition_distance must be approximately 30.7367, with an absolute tolerance of ±1.5 (inclusive). The displayed reference is rounded for readability; the original contract retains the exact value.
Does not earn credit
No credit for a missing field, a value that is not a finite JSON number, or a result outside the allowed tolerance.
Accepted alternatives
Evidence-backed numerical interval covers the separately computed mapping and aggregation sensitivity estimates; no method declaration or prose is graded.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.mean_composition_distance; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.mean_composition_distance; q20.mean_composition_distance
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Failed. Submitted mean_composition_distance = 28.1035; reference ≈ 30.7367. Absolute difference ≈ 2.63317; allowed difference ±1.5. Displayed numbers are rounded; the verdict is the original recorded result.
Gene symbols for every AP-1 member that has the largest treated/vehicle fold ratio of nuclear-coding-pool-relative RNA signal at any individual treated dose
Earns credit
The response_leaders field equals ['FOSL2', 'JUND'] after supported identifier normalization.
Does not earn credit
The field is missing, null, invalid, or fails the shared deterministic comparison.
Accepted alternatives
Order does not affect the set comparison. Repeated members, including aliases of the same member, fail the check. Leading and trailing whitespace is ignored. Accepted aliases: ENSG00000075426.12 → FOSL2; ENSG00000075426 → FOSL2; fosl2 → FOSL2; ENSG00000130522.6 → JUND; ENSG00000130522 → JUND; jund → JUND.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.response_leaders; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.response_leaders; q20.response_leaders
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Passed. response_leaders: matched 2 of 2 reference members. No missing or extra members.
Treatment-average divided by vehicle for the summed nuclear-coding-pool-normalized signal of all seven core AP-1 members
Earns credit
In the submitted JSON, system_ratio must be approximately 0.576121, with an absolute tolerance of ±0.06 (inclusive). The displayed reference is rounded for readability; the original contract retains the exact value.
Does not earn credit
No credit for a missing field, a value that is not a finite JSON number, or a result outside the allowed tolerance.
Accepted alternatives
Evidence-backed numerical interval covers the separately computed mapping and aggregation sensitivity estimates; no method declaration or prose is graded.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.system_ratio; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.system_ratio; q20.system_ratio
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Passed. Submitted system_ratio = 0.6183; reference ≈ 0.576121. Absolute difference ≈ 0.0421792; allowed difference ±0.06. Displayed numbers are rounded; the verdict is the original recorded result.
Total AP-1 signal in the 1 nM condition divided by vehicle: ratio of the condition means of summed nuclear-coding-pool-relative RNA signal
Earns credit
In the submitted JSON, pool_ratio_1nm must be approximately 0.894321, with an absolute tolerance of ±0.05 (inclusive). The displayed reference is rounded for readability; the original contract retains the exact value.
Does not earn credit
No credit for a missing field, a value that is not a finite JSON number, or a result outside the allowed tolerance.
Accepted alternatives
Evidence-backed numerical interval covers the separately computed mapping and aggregation sensitivity estimates; no method declaration or prose is graded.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.pool_ratio_1nm; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.pool_ratio_1nm; q20.pool_ratio_1nm
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Passed. Submitted pool_ratio_1nm = 0.872405; reference ≈ 0.894321. Absolute difference ≈ 0.0219166; allowed difference ±0.05. Displayed numbers are rounded; the verdict is the original recorded result.
Total AP-1 signal in the 10 nM condition divided by vehicle: ratio of the condition means of summed nuclear-coding-pool-relative RNA signal
Earns credit
In the submitted JSON, pool_ratio_10nm must be approximately 0.39956, with an absolute tolerance of ±0.025 (inclusive). The displayed reference is rounded for readability; the original contract retains the exact value.
Does not earn credit
No credit for a missing field, a value that is not a finite JSON number, or a result outside the allowed tolerance.
Accepted alternatives
Evidence-backed numerical interval covers the separately computed mapping and aggregation sensitivity estimates; no method declaration or prose is graded.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.pool_ratio_10nm; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.pool_ratio_10nm; q20.pool_ratio_10nm
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Failed. Submitted pool_ratio_10nm = 0.454354; reference ≈ 0.39956. Absolute difference ≈ 0.0547936; allowed difference ±0.025. Displayed numbers are rounded; the verdict is the original recorded result.
Total AP-1 signal in the 100 nM condition divided by vehicle: ratio of the condition means of summed nuclear-coding-pool-relative RNA signal
Earns credit
In the submitted JSON, pool_ratio_100nm must be approximately 0.490327, with an absolute tolerance of ±0.035 (inclusive). The displayed reference is rounded for readability; the original contract retains the exact value.
Does not earn credit
No credit for a missing field, a value that is not a finite JSON number, or a result outside the allowed tolerance.
Accepted alternatives
Evidence-backed numerical interval covers the separately computed mapping and aggregation sensitivity estimates; no method declaration or prose is graded.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.pool_ratio_100nm; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.pool_ratio_100nm; q20.pool_ratio_100nm
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Failed. Submitted pool_ratio_100nm = 0.581505; reference ≈ 0.490327. Absolute difference ≈ 0.0911779; allowed difference ±0.035. Displayed numbers are rounded; the verdict is the original recorded result.
Total AP-1 signal in the 1000 nM condition divided by vehicle: ratio of the condition means of summed nuclear-coding-pool-relative RNA signal
Earns credit
In the submitted JSON, pool_ratio_1000nm must be approximately 0.520273, with an absolute tolerance of ±0.04 (inclusive). The displayed reference is rounded for readability; the original contract retains the exact value.
Does not earn credit
No credit for a missing field, a value that is not a finite JSON number, or a result outside the allowed tolerance.
Accepted alternatives
Evidence-backed numerical interval covers the separately computed mapping and aggregation sensitivity estimates; no method declaration or prose is graded.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.pool_ratio_1000nm; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.pool_ratio_1000nm; q20.pool_ratio_1000nm
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Failed. Submitted pool_ratio_1000nm = 0.564935; reference ≈ 0.520273. Absolute difference ≈ 0.0446619; allowed difference ±0.04. Displayed numbers are rounded; the verdict is the original recorded result.
Descriptive fraction of library-level total AP-1 signal variation explained by the five condition means, including vehicle
Earns credit
In the submitted JSON, pool_dose_eta2 must be approximately 0.878836, with an absolute tolerance of ±0.025 (inclusive). The displayed reference is rounded for readability; the original contract retains the exact value.
Does not earn credit
No credit for a missing field, a value that is not a finite JSON number, or a result outside the allowed tolerance.
Accepted alternatives
Evidence-backed numerical interval covers the separately computed mapping and aggregation sensitivity estimates; no method declaration or prose is graded.
Weight: 1
Input evidence
Complete three-million-read subset · Each library contributes to the condition mean and the full reference transcriptional pool.
Reference evidence
reference-analysis-v2 · variants.q0_equal.pool_dose_eta2; all nine variants; diagnostics
Recomputed endpoint from cached exact-input counts for all ten libraries; independent profile calculation agrees for both q0 and q20.
independent-endpoints-v2 · q0.pool_dose_eta2; q20.pool_dose_eta2
Separate implementation; eta-squared also verified by one minus within-condition SS divided by total SS.
Recorded result / GPT 6 astra
Failed. Submitted pool_dose_eta2 = 0.840883; reference ≈ 0.878836. Absolute difference ≈ 0.0379535; allowed difference ±0.025. Displayed numbers are rounded; the verdict is the original recorded result.