Q (haiku): show me gbm with mgmt hypermethylation ▶ resolve_and_route { "studyKeywords": [ "GBM", "glioblastoma" ] } ▶ search_oncotree { "search_term": "GBM" } ◀ result {"success":true,"message":"Found 8 matching studies (top 5 with full metadata, rest with basic info). 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":8,"studiesWithMetadata":[{"studyId":"gbm_tcga","name":"Glioblastoma Multiforme (TCGA, Firehose Legacy)","sampleCount":619,"studyViewUrl":"https://www.cbioportal.org/study?id=gbm_tcga","metadata":{"clinicalAttributeIds":["AGE","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","ETHNICITY","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","HISTOLOGICAL_DIAGNOSIS","HISTORY_LGG_DX_OF_BRAIN_TISSUE","HISTORY_NEOADJUVANT_TRTYN","HISTORY_OTHER_MALIGNANCY","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","INITIAL_PATHOLOGIC_DX_YEAR","IS_FFPE","KARNOFSKY_PERFORMANCE_SCORE","LONGEST_DIMENSION","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT","METHOD_OF_INITIAL_SAMPLE_PROCUREMENT_OTHER","METHOD_OF_SAMPLE_PROCUREMENT","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_TIMING","PHARMACEUTICAL_TX_ADJUVANT","PRIMARY_SITE_PATIENT","PROJECT_CODE","PROSPECTIVE_COLLECTION","RACE","RADIATION_TREATMENT_ADJUVANT","RETROSPECTIVE_COLLECTION","SAMPLE_COUNT","SAMPLE_INITIAL_WEIGHT","SAMPLE_TYPE","SAMPLE_TYPE_ID","SEX","SHORTEST_DIMENSION","SITE_OF_TUMOR_TISSUE","SOMATIC_STATUS","SPECIMEN_CURRENT_WEIGHT","SPECIMEN_FREEZING_METHOD","SPECIMEN_SECOND_LONGEST_DIMENSION","TIME_BETWEEN_CLAMPING_AND_FREEZING","TIME_BETWEEN_EXCISION_AND_FREEZING","TISSUE_SOURCE_SITE","TMB_NONSYNONYMOUS","TREATMENT_OUTCOME_FIRST_COURSE","TUMOR_STATUS","VIAL_NUMBER"],"molecularProfileIds":["gbm_tcga_gistic","gbm_tcga_linear_CNA","gbm_tcga_methylation_hm27","gbm_tcga_methylation_hm450","gbm_tcga_mrna","gbm_tcga_mrna_U133","gbm_tcga_mrna_U133_Zscores","gbm_tcga_mrna_U133_all_sample_Zscores","gbm_tcga_mrna_median_Zscores","gbm_tcga_mrna_median_all_sample_Zscores","gbm_tcga_mutations","gbm_tcga_rna_seq_v2_mrna","gbm_tcga_rna_seq_v2_mrna_median_Zscores","gbm_tcga_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_rppa","gbm_tcga_rppa_Zscores"],"heatmapProfileIds":["gbm_tcga_methylation_hm27","gbm_tcga_methylation_hm450","gbm_tcga_mrna_U133_Zscores","gbm_tcga_mrna_U133_all_sample_Zscores","gbm_tcga_mrna_median_Zscores","gbm_tcga_mrna_median_all_sample_Zscores","gbm_tcga_rna_seq_v2_mrna_median_Zscores","gbm_tcga_rna_seq_v2_mrna_median_all_sample_Zscores","gbm_tcga_rppa_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna","protein","dna_methylation"]}},{"studyId":"gbm_tcga_gdc","name":"Glioblastoma Multif … (6771 more chars) ◀ result {"result":[{"code":"GB","name":"Glioblastoma, IDH-Wildtype","score":90,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > GB","replacedCodes":["GBM"]},{"code":"SCGBM","name":"Small Cell Glioblastoma","score":55,"mainType":"Glioma","tissue":"CNS/Brain","hierarchy":"BRAIN > DIFG > ADIFG > GB > SCGBM"}]} ▶ clickhouse_list_tables {} ◀ result {"tables":[{"name":"allele_specific_copy_number"},{"name":"alteration_driver_annotation"},{"name":"cancer_study"},{"name":"cancer_study_query_preferences"},{"name":"cancer_study_tags"},{"name":"cbioportal_sequence_state"},{"name":"clinical_attribute_counts"},{"name":"clinical_attribute_meta"},{"name":"clinical_data_derived"},{"name":"clinical_event"},{"name":"clinical_event_data"},{"name":"clinical_event_data_derived"},{"name":"clinical_event_derived"},{"name":"clinical_patient"},{"name":"clinical_sample"},{"name":"cna_event"},{"name":"cna_panel_gene_coverage"},{"name":"cna_wes_coverage"},{"name":"co_altered_genes_in_study"},{"name":"copy_number_seg"},{"name":"copy_number_seg_file"},{"name":"gene"},{"name":"gene_alias"},{"name":"gene_alteration_frequency_by_cancer_type"},{"name":"gene_cna_distribution_in_study"},{"name":"gene_mutation_frequency_by_cancer_type"},{"name":"gene_mutation_frequency_in_studies"},{"name":"gene_mutation_frequency_in_study"},{"name":"gene_mutation_variants_in_study"},{"name":"gene_pair_coexpression"},{"name":"gene_panel"},{"name":"gene_panel_list"},{"name":"gene_panel_to_gene_derived"},{"name":"generic_assay_data_derived"},{"name":"generic_assay_meta_derived"},{"name":"generic_assay_profile_entity_derived"},{"name":"generic_entity_properties"},{"name":"geneset"},{"name":"geneset_gene"},{"name":"geneset_hierarchy_leaf"},{"name":"geneset_hierarchy_node"},{"name":"genetic_alteration"},{"name":"genetic_alteration_derived"},{"name":"genetic_entity"},{"name":"genetic_profile"},{"name":"genetic_profile_link"},{"name":"genetic_profile_samples"},{"name":"genomic_event_derived"},{"name":"gistic"},{"name":"gistic_to_gene"},{"name":"info"},{"name":"mut_sig"},{"name":"mutation"},{"name":"mutation_count_by_keyword"},{"name":"mutation_derived"},{"name":"mutation_event"},{"name":"mutation_panel_gene_coverage"},{"name":"mutation_wes_coverage"},{"name":"patient"},{"name":"reference_genome"},{"name":"reference_genome_gene"},{"name":"resource_definition"},{"name":"resource_patient"},{"name":"resource_sample"},{"name":"resource_study"},{"name":"sample"},{"name":"sample_cna_event"},{"name":"sample_derived"},{"name":"sample_list"},{"name":"sample_list_list"},{"name":"sample_profile"},{"name":"sample_to_gene_panel_derived"},{"name":"structural_variant"},{"name":"sv_panel_gene_coverage"},{"name":"sv_wes_coverage"},{"name":"top_cna_genes_in_study"},{"name":"top_mutated_genes_in_cohort"},{"name":"top_mutated_genes_in_study"},{"name":"top_sv_genes_in_study"},{"name":"treatment_counts_in_study"},{"name":"treatment_regimens_in_study"},{"name":"type_of_cancer"}]} ▶ get_studyviewfilter_options { "studyId": "gbm_tcga_pan_can_atlas_2018", "entitySearch": "MGMT", "genericAssayProfileIds": [ "gbm_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge", "gbm_tcga_pan_can_atlas_2018_methylation_hm450" ] } ◀ result {"success":false,"error":"Not Found","details":{"status":404,"response":{"req":{"method":"POST","url":"https://www.cbioportal.org/api/generic_assay_meta/fetch","data":{"molecularProfileIds":["gbm_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge"]},"headers":{"user-agent":"node-superagent/3.8.3","accept":"application/json","content-type":"application/json"}},"header":{"cache-control":"no-cache, no-store, max-age=0, must-revalidate","content-encoding":"gzip","content-type":"application/json","date":"Fri, 25 Sep 2026 01:07:12 GMT","elapsed-time":"1","expires":"0","pragma":"no-cache","strict-transport-security":"max-age=31536000 ; includeSubDomains","vary":"origin,access-control-request-method,access-control-request-headers,accept-encoding","x-content-type-options":"nosniff","x-frame-options":"DENY","x-xss-protection":"0","connection":"close","transfer-encoding":"chunked"},"status":404,"text":"{\"timestamp\":1790298432966,\"status\":404,\"error\":\"Not Found\",\"path\":\"/api/generic_assay_meta/fetch\"}"}}} ▶ clickhouse_list_table_columns { "table": "generic_assay_data_derived" } ◀ result {"columns":[{"name":"sample_unique_id","type":"String"},{"name":"patient_unique_id","type":"String"},{"name":"genetic_entity_id","type":"String"},{"name":"value","type":"String"},{"name":"generic_assay_type","type":"String"},{"name":"profile_stable_id","type":"String"},{"name":"entity_stable_id","type":"String"},{"name":"datatype","type":"String"},{"name":"patient_level","type":"Decimal(10, 0)"},{"name":"profile_type","type":"String"}]} ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT genetic_profile_id, profile_name FROM genetic_profile WHERE cancer_study_id = (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'gbm_tcga_pan_can_atlas_2018') AND genetic_alteration_type = 'METHYLATION' LIMIT 10 " } ◀ result {"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Unknown expression identifier `profile_name` in scope SELECT DISTINCT genetic_profile_id, profile_name FROM genetic_profile WHERE (cancer_study_id = (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'gbm_tcga_pan_can_atlas_2018')) AND (genetic_alteration_type = 'METHYLATION') LIMIT 10. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_list_table_columns { "table": "genetic_profile" } ◀ result {"columns":[{"name":"genetic_profile_id","type":"Int64"},{"name":"stable_id","type":"String"},{"name":"cancer_study_id","type":"Int64"},{"name":"genetic_alteration_type","type":"String"},{"name":"generic_assay_type","type":"Nullable(String)"},{"name":"datatype","type":"String"},{"name":"name","type":"String"},{"name":"description","type":"Nullable(String)"},{"name":"show_profile_in_analysis_tab","type":"Int32"},{"name":"pivot_threshold","type":"Nullable(Float64)"},{"name":"sort_order","type":"Nullable(String)"},{"name":"patient_level","type":"Nullable(Int32)"}]} ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT profile_stable_id, generic_assay_type FROM generic_assay_data_derived WHERE profile_stable_id LIKE '%gbm_tcga_pan_can_atlas_2018%methylation%' LIMIT 10 " } ◀ result {"error_message":"Query timed out after 30 seconds"} ▶ clickhouse_run_select_query { "query": " SELECT COUNT(*) AS total_samples, SUM(CASE WHEN value LIKE '%hypermethylated%' OR value LIKE '%Methylated%' THEN 1 ELSE 0 END) AS methylated_count FROM generic_assay_data_derived WHERE profile_stable_id IN ('gbm_tcga_pan_can_atlas_2018_methylation_hm450', 'gbm_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge') AND entity_stable_id = 'MGMT' ", "max_rows": 100 } ◀ result {"rows":[{"total_samples":0,"methylated_count":0}]} ▶ clickhouse_run_select_query { "query": " SELECT DISTINCT profile_stable_id, entity_stable_id, COUNT(*) as sample_count FROM generic_assay_data_derived WHERE profile_stable_id LIKE 'gbm_tcga_pan_can_atlas_2018_methylation%' GROUP BY profile_stable_id, entity_stable_id ORDER BY sample_count DESC LIMIT 20 ", "max_rows": 100 } ◀ result {"error_message":"Query timed out after 30 seconds"} ▶ navigate_to_study_view { "studyIds": [ "gbm_tcga_pub2013" ], "filterAttributeId": "MGMT_STATUS", "filterValues": "hypermethylated", "tab": "summary" } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013&filterAttributeId=MGMT_STATUS&filterValues=hypermethylated","url":"https://www.cbioportal.org/study/summary?id=gbm_tcga_pub2013&filterAttributeId=MGMT_STATUS&filterValues=hypermethylated","data":{"studyIds":["gbm_tcga_pub2013"],"studies":[{"studyId":"gbm_tcga_pub2013","name":"Glioblastoma (TCGA, Cell 2013)","sampleCount":577}],"tab":"summary","hasFilters":true,"hasPlotsConfig":false,"pageDescription":"Overview of all study data displayed as interactive charts summarizing available clinical and genomic data. Click within a chart to filter. Additional charts may be available in the Charts menu."}} ▶ clickhouse_run_select_query { "query": " SELECT attribute_value, COUNT(DISTINCT sample_id) as sample_count FROM clinical_data_derived WHERE cancer_study_id = (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'gbm_tcga_pub2013') AND attribute_name = 'MGMT_STATUS' GROUP BY attribute_value ORDER BY sample_count DESC ", "max_rows": 100 } ◀ result {"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Unknown expression or function identifier `sample_id` in scope SELECT attribute_value, COUNTDistinct(sample_id) AS sample_count FROM clinical_data_derived WHERE (cancer_study_id = (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'gbm_tcga_pub2013')) AND (attribute_name = 'MGMT_STATUS') GROUP BY attribute_value ORDER BY sample_count DESC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_list_table_columns { "table": "clinical_data_derived" } ◀ result {"columns":[{"name":"internal_id","type":"Int32"},{"name":"sample_unique_id","type":"String","comment":"Globally unique sample ID: cancer_study_identifier + \"_\" + sample.stable_id. Empty for patient-level attributes. Use this for sample filtering and joins."},{"name":"patient_unique_id","type":"String","comment":"Globally unique patient ID: cancer_study_identifier + \"_\" + patient.stable_id. Present for both sample and patient-level attributes."},{"name":"attribute_name","type":"LowCardinality(String)","comment":"Clinical attribute name (e.g., SAMPLE_TYPE, CANCER_TYPE, AGE, OS_MONTHS). Use with attribute_value for filtering. AGE may be floored or capped for de-identification (e.g. all children recorded as 18, or everyone 89+ recorded as 89 or 90): before age statistics check for a pile-up at the min/max, and if present compute age from DAYS_TO_BIRTH (-days / 365.25)."},{"name":"attribute_value","type":"String","comment":"Value of the clinical attribute (String). For SAMPLE_TYPE: Primary, Metastasis, Local Recurrence, Unknown. Missing values are empty strings, so use toFloat64OrNull(attribute_value) for numeric comparisons — CAST fails on them."},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"type","type":"LowCardinality(String)","comment":"Data level: \"sample\" for sample-level attributes (e.g., SAMPLE_TYPE), \"patient\" for patient-level attributes (e.g., AGE, OS_MONTHS)."}]} ▶ clickhouse_run_select_query { "query": " SELECT attribute_value, COUNT(DISTINCT sample_unique_id) as sample_count FROM clinical_data_derived WHERE cancer_study_id = (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'gbm_tcga_pub2013') AND attribute_name = 'MGMT_STATUS' GROUP BY attribute_value ORDER BY sample_count DESC ", "max_rows": 100 } ◀ result {"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Unknown expression or function identifier `cancer_study_id` in scope SELECT attribute_value, COUNTDistinct(sample_unique_id) AS sample_count FROM clinical_data_derived WHERE (cancer_study_id = (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'gbm_tcga_pub2013')) AND (attribute_name = 'MGMT_STATUS') GROUP BY attribute_value ORDER BY sample_count DESC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_run_select_query { "query": " SELECT attribute_value, COUNT(DISTINCT sample_unique_id) as sample_count FROM clinical_data_derived WHERE cancer_study_identifier = 'gbm_tcga_pub2013' AND attribute_name = 'MGMT_STATUS' GROUP BY attribute_value ORDER BY sample_count DESC ", "max_rows": 100 } ◀ result {"rows":[{"sample_count":227},{"attribute_value":"UNMETHYLATED","sample_count":180},{"attribute_value":"METHYLATED","sample_count":170}]} ▶ navigate_to_results_view { "studyIds": [ "gbm_tcga_pub2013" ], "genes": [ "TP53", "IDH1", "EGFR", "PTEN" ], "studyViewFilter": { "clinicalDataFilters": [ { "attributeId": "MGMT_STATUS", "values": [ { "value": "METHYLATED" } ] } ] }, "tab": "oncoprint" } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/results/oncoprint?session_id=6ab5c996e497aad53593c270","url":"https://www.cbioportal.org/results/oncoprint?session_id=6ab5c996e497aad53593c270","data":{"studyIds":["gbm_tcga_pub2013"],"studies":[{"studyId":"gbm_tcga_pub2013","name":"Glioblastoma (TCGA, Cell 2013)","sampleCount":577}],"genes":["TP53","IDH1","EGFR","PTEN"],"filteredSampleCount":170,"caseSetId":"-1","sessionId":"6ab5c996e497aad53593c270","studyViewUrl":"https://www.cbioportal.org/study?id=gbm_tcga_pub2013#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MGMT_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22METHYLATED%22%7D%5D%7D%5D%7D","pageDescription":"Visual summary of alterations in queried genes across samples."}} ▶ navigate_to_group_comparison { "studyIds": [ "gbm_tcga_pub2013" ], "groups": [ { "name": "MGMT Hypermethylated", "studyViewFilter": { "clinicalDataFilters": [ { "attributeId": "MGMT_STATUS", "values": [ { "value": "METHYLATED" } ] } ] } }, { "name": "MGMT Unmethylated", "studyViewFilter": { "clinicalDataFilters": [ { "attributeId": "MGMT_STATUS", "values": [ { "value": "UNMETHYLATED" } ] } ] } } ], "tab": "survival" } ◀ result {"success":true,"message":"Navigating to https://www.cbioportal.org/comparison/survival?comparisonId=6ab5c998e497aad53593c271","url":"https://www.cbioportal.org/comparison/survival?comparisonId=6ab5c998e497aad53593c271","data":{"description":"Group comparison (2 custom groups)","studies":["gbm_tcga_pub2013"],"totalGroups":2,"groups":[{"name":"MGMT Hypermethylated","sampleCount":170},{"name":"MGMT Unmethylated","sampleCount":180}],"studyViewUrl":"https://www.cbioportal.org/study?id=gbm_tcga_pub2013","groupUrls":[{"groupName":"MGMT Hypermethylated","url":"https://www.cbioportal.org/study?id=gbm_tcga_pub2013#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MGMT_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22METHYLATED%22%7D%5D%7D%5D%7D"},{"groupName":"MGMT Unmethylated","url":"https://www.cbioportal.org/study?id=gbm_tcga_pub2013#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22MGMT_STATUS%22%2C%22values%22%3A%5B%7B%22value%22%3A%22UNMETHYLATED%22%7D%5D%7D%5D%7D"}],"pageDescription":"Kaplan-Meier survival analysis comparing MGMT Hypermethylated (170) vs MGMT Unmethylated (180)."}} ═ answer (success) Perfect! Here's what I found for GBM with MGMT hypermethylation: ## Summary **Study:** Glioblastoma (TCGA, Cell 2013) – 577 total samples - **MGMT Hypermethylated:** 170 samples (29.5%) - **MGMT Unmethylated:** 180 samples (31.2%) - **MGMT Status Unknown:** 227 samples (39.3%) --- ## Analysis Links **[View MGMT-methylated GBM with OncoPrint](https://www.cbioportal.org/results/oncoprint?session_id=6ab5c996e497aad53593c270)** - Filtered to 170 MGMT-hypermethylated samples - Shows alterations in TP53, IDH1, EGFR, PTEN - Visual summary (OncoPrint) of genomic alterations across samples **[Compare MGMT Hypermethylated vs Unmethylated — Survival Analysis](https://www.cbioportal.org/comparison/survival?comparisonId=6ab5c998e497aad53593c271)** - Kaplan-Meier survival curves comparing groups - MGMT Hypermethylated: 170 samples - MGMT Unmethylated: 180 samples - Statistical analysis of survival differences --- ## Alternative Studies If you need methylation probe-level data, **GBM (TCGA, PanCancer Atlas)** has HM27 and HM450 methylation arrays available but requires probe-specific MGMT queries. The Cell 2013 study provides the cleaner MGMT_STATUS clinical classification above.