Q (haiku): In TCGA lower grade glioma, show me IDH1 mRNA expression by IDH1 mutation status.

▶ resolve_and_route
{
 "studyKeywords": [
  "TCGA",
  "lower grade glioma"
 ]
}

◀ result
{"success":true,"message":"Found 2 matching studies. Pick the best match (prefer TCGA → prefer PanCancer Atlas), use its metadata to call the appropriate navigation tool(s) and generate URLs immediately. Present other studies as alternatives.","data":{"totalCount":2,"studiesWithMetadata":[{"studyId":"lgg_tcga","name":"Brain Lower Grade Glioma (TCGA, Firehose Legacy)","sampleCount":530,"studyViewUrl":"https://www.cbioportal.org/study?id=lgg_tcga","metadata":{"clinicalAttributeIds":["AGE","ANIMAL_INSECT_ALLERGY_AGE","ANIMAL_INSECT_ALLERGY_HIST","ASTHMA_ECZEMA_ALLERGY_FIRST_DIAGNOSIS","ASTHMA_HISTORY","CANCER_TYPE","CANCER_TYPE_DETAILED","DAYS_TO_COLLECTION","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DAYS_TO_SPECIMEN_COLLECTION","DFS_MONTHS","DFS_STATUS","DISEASE_CODE","ECOG_SCORE","ECZEMA_HISTORY","ETHNICITY","FAMILY_HISTORY_OF_CANCER","FAMILY_HISTORY_OF_PRIMARY_BRAIN_TUMOR","FIRST_SYMPTOM_LONGEST_DURATION","FOOD_ALLERGY_AGE","FOOD_ALLERGY_HISTORY","FOOD_ALLERGY_TYPES","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","GRADE","HAY_FEVER_HISTORY","HEADACHE_HISTORY","HISTOLOGICAL_DIAGNOSIS","HISTORY_IONIZING_RT_TO_HEAD","HISTORY_NEOADJUVANT_MEDICATION","HISTORY_NEOADJUVANT_STEROID_TX","HISTORY_NEOADJUVANT_TRTYN","HISTORY_OTHER_MALIGNANCY","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","IDH1_MUTATION","IDH1_MUTATION_TEST_INDICATOR","IDH1_MUTATION_TEST_METHOD","INFORMED_CONSENT_VERIFIED","INHERITED_GENETIC_SYNDROME_INDICATOR","INHERITED_GENETIC_SYNDROME_SPECIFIED","INITIAL_PATHOLOGIC_DX_YEAR","IS_FFPE","KARNOFSKY_PERFORMANCE_SCORE","LATERALITY","LONGEST_DIMENSION","METHOD_OF_SAMPLE_PROCUREMENT","MOLD_OR_DUST_ALLERGY_HISTORY","MUTATION_COUNT","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","OCT_EMBEDDED","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_METHOD_OF_SAMPLE_PROCUREMENT","OTHER_PATIENT_ID","OTHER_SAMPLE_ID","PATHOLOGY_REPORT_FILE_NAME","PATHOLOGY_REPORT_UUID","PERFORMANCE_STATUS_DAYS_TO","PERFORMANCE_STATUS_TIMING","PROJECT_CODE","PROSPECTIVE_COLLECTION","RACE","RADIATION_TREATMENT_ADJUVANT","RELATED_SYMPTOM_FIRST_PRESENT","RETROSPECTIVE_COLLECTION","SAMPLE_COUNT","SAMPLE_INITIAL_WEIGHT","SAMPLE_TYPE","SAMPLE_TYPE_ID","SEIZURE_HISTORY","SEX","SHORTEST_DIMENSION","SITE_OF_TUMOR_TISSUE","SOMATIC_STATUS","SPECIMEN_CURRENT_WEIGHT","SPECIMEN_FREEZING_METHOD","SPECIMEN_SECOND_LONGEST_DIMENSION","SUPRATENTORIAL_LOCALIZATION","SYMP_CHANGES_MENTAL_STATUS","SYMP_CHANGES_MOTOR_MOVEMENT","SYMP_CHANGES_SENSORY","SYMP_CHANGES_VISUAL","TARGETED_MOLECULAR_THERAPY","TIME_BETWEEN_CLAMPING_AND_FREEZING","TIME_BETWEEN_EXCISION_AND_FREEZING","TISSUE_SOURCE_SITE","TMB_NONSYNONYMOUS","TREATMENT_OUTCOME_FIRST_COURSE","TUMOR_SITE","TUMOR_STATUS","VIAL_NUMBER"],"molecularProfileIds":["lgg_tcga_gistic","lgg_tcga_linear_CNA","lgg_tcga_methylation_hm450","lgg_tcga_mrna","lgg_tcga_mrna_median_Zscores","lgg_tcga_mrna_median_all_sample_Zscores","lgg_tcga_mutations","lgg_tcga_rna_seq_v2_mrna","lgg_tcga_rna_seq_v2_mrna_median_Zscores","lgg_tcga_rna_seq_v2_mrna_median_all_sample_Zscores","lg … (2867 more chars)

▶ navigate_to_group_comparison
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ],
 "groups": [
  {
   "name": "IDH1 Mutated",
   "studyViewFilter": {
    "mutationDataFilters": [
     {
      "hugoGeneSymbol": "IDH1",
      "profileType": "mutations",
      "categorization": "MUTATED",
      "values": [
       [
        {
         "value": "MUTATED"
        }
       ]
      ]
     }
    ]
   }
  },
  {
   "name": "IDH1 Wildtype",
   "studyViewFilter": {
    "mutationDataFilters": [
     {
      "hugoGeneSymbol": "IDH1",
      "profileType": "mutations",
      "categorization": "MUTATED",
      "values": [
       [
        {
         "value": "NOT_MUTATED"
        }
       ]
      ]
     }
    ]
   }
  }
 ],
 "tab": "mrna"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/comparison/mrna?comparisonId=6ab7f957c2115c492d885153","url":"https://www.cbioportal.org/comparison/mrna?comparisonId=6ab7f957c2115c492d885153","data":{"description":"Group comparison (2 custom groups)","studies":["lgg_tcga_pan_can_atlas_2018"],"totalGroups":2,"groups":[{"name":"IDH1 Mutated","sampleCount":395},{"name":"IDH1 Wildtype","sampleCount":119}],"studyViewUrl":"https://www.cbioportal.org/study?id=lgg_tcga_pan_can_atlas_2018","groupUrls":[{"groupName":"IDH1 Mutated","url":"https://www.cbioportal.org/study?id=lgg_tcga_pan_can_atlas_2018#filterJson=%7B%22mutationDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22IDH1%22%2C%22profileType%22%3A%22mutations%22%2C%22categorization%22%3A%22MUTATED%22%2C%22values%22%3A%5B%5B%7B%22value%22%3A%22MUTATED%22%7D%5D%5D%7D%5D%7D"},{"groupName":"IDH1 Wildtype","url":"https://www.cbioportal.org/study?id=lgg_tcga_pan_can_atlas_2018#filterJson=%7B%22mutationDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22IDH1%22%2C%22profileType%22%3A%22mutations%22%2C%22categorization%22%3A%22MUTATED%22%2C%22values%22%3A%5B%5B%7B%22value%22%3A%22NOT_MUTATED%22%7D%5D%5D%7D%5D%7D"}],"pageDescription":"mRNA expression for all genes compared across IDH1 Mutated (395) vs IDH1 Wildtype (119)."}}

═ answer (success)
Perfect! I've set up a group comparison for you:

**[View IDH1 mRNA Expression by IDH1 Mutation Status](https://www.cbioportal.org/comparison/mrna?comparisonId=6ab7f957c2115c492d885153)**

This comparison includes:
- **IDH1 Mutated:** 395 samples
- **IDH1 Wildtype:** 119 samples

The mRNA tab will show IDH1 expression levels (as z-scores) overlaid for both groups, allowing you to directly visualize how IDH1 mutation status correlates with IDH1 transcript abundance. You'll see box plots, individual sample values, and statistical comparison across all genes between the two mutation groups.