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)

▶ get_studyviewfilter_options
{
 "studyId": "lgg_tcga_pan_can_atlas_2018",
 "geneSpecificQueries": [
  {
   "hugoGeneSymbol": "IDH1",
   "profileType": "mutations"
  }
 ]
}

◀ result
{"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"lgg_tcga_pan_can_atlas_2018","geneSpecificCounts":[{"hugoGeneSymbol":"IDH1","profileType":"mutations","counts":[{"value":"Missense_Mutation","label":"Missense Mutation","count":395}]}]}}

▶ navigate_to_results_view
{
 "studyIds": [
  "lgg_tcga_pan_can_atlas_2018"
 ],
 "genes": [
  "IDH1"
 ],
 "tab": "plots",
 "plotsVertSelection": {
  "selectedGeneOption": "IDH1",
  "dataType": "mRNA_expression",
  "selectedDataSourceOption": "lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores"
 },
 "plotsHorzSelection": {
  "selectedGeneOption": "IDH1",
  "dataType": "mutation",
  "mutationCountBy": "mutationType"
 }
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/plots?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=IDH1&case_set_id=lgg_tcga_pan_can_atlas_2018_all&plots_horz_selection=%7B%22selectedGeneOption%22%3A%223417%22%2C%22dataType%22%3A%22mutation%22%2C%22mutationCountBy%22%3A%22mutationType%22%7D&plots_vert_selection=%7B%22selectedGeneOption%22%3A%223417%22%2C%22dataType%22%3A%22mRNA_expression%22%2C%22selectedDataSourceOption%22%3A%22lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores%22%7D","url":"https://www.cbioportal.org/results/plots?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=IDH1&case_set_id=lgg_tcga_pan_can_atlas_2018_all&plots_horz_selection=%7B%22selectedGeneOption%22%3A%223417%22%2C%22dataType%22%3A%22mutation%22%2C%22mutationCountBy%22%3A%22mutationType%22%7D&plots_vert_selection=%7B%22selectedGeneOption%22%3A%223417%22%2C%22dataType%22%3A%22mRNA_expression%22%2C%22selectedDataSourceOption%22%3A%22lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores%22%7D","data":{"studyIds":["lgg_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","sampleCount":514}],"genes":["IDH1"],"caseSetId":"lgg_tcga_pan_can_atlas_2018_all","pageDescription":"Scatter/box plots: IDH1 mrna_expression (y-axis) by IDH1 mutation (x-axis)."}}

═ answer (success)
Perfect! Here's your visualization:

[**View IDH1 mRNA Expression by IDH1 Mutation Status**](https://www.cbioportal.org/results/plots?cancer_study_list=lgg_tcga_pan_can_atlas_2018&gene_list=IDH1&case_set_id=lgg_tcga_pan_can_atlas_2018_all&plots_horz_selection=%7B%22selectedGeneOption%22%3A%223417%22%2C%22dataType%22%3A%22mutation%22%2C%22mutationCountBy%22%3A%22mutationType%22%7D&plots_vert_selection=%7B%22selectedGeneOption%22%3A%223417%22%2C%22dataType%22%3A%22mRNA_expression%22%2C%22selectedDataSourceOption%22%3A%22lgg_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores%22%7D)

**Study:** Brain Lower Grade Glioma (TCGA, PanCancer Atlas) — 514 samples

**Configuration:**
- **Y-axis:** IDH1 mRNA expression (Z-scores)
- **X-axis:** IDH1 mutation status (395 samples with IDH1 missense mutations)

The scatter/box plot will display IDH1 mRNA levels stratified by mutation presence, allowing you to see if IDH1 mutations correlate with altered expression patterns.