Q (haiku): Can you please generate a survival curve for colorectal cancer patients based on the expression levels of IMPDH2? ▶ read_guide { "uri": "cbioportal://statistical-tests-guide" } ▶ list_studies { "search": "colorectal cancer", "limit": 20 } ◀ result Statistical Test Selection Guide ================================ Purpose ------- This guide ensures the correct statistical test is selected before performing any group comparison, matching cBioPortal's own Group Comparison defaults. HARD RULES — NEVER FABRICATE A STATISTIC ---------------------------------------- ClickHouse cannot run statistical tests. The agent therefore must NEVER produce a derived statistic that is not a literal column value from a SQL result. Specifically: 1. **Never invent a p-value.** Not "p < 0.001", not "p ≈ 0.05", not any p-value. If the user asks "what is the p-value?", the answer is *"I can't compute that — here is the 2x2 contingency table (or group statistics). Run it in cBioPortal's Group Comparison tab, in R with `fisher.test(...)` / `wilcox.test(...)`, or in Python with `scipy.stats.fisher_exact(...)` / `mannwhitneyu(...)`."* 2. **Never claim mutual exclusivity (or co-occurrence) from a contingency table alone.** A 2x2 table is not a test. The shape "altered/not altered × group A/group B" needs Fisher's exact + a defined direction (odds ratio < 1 with significant p). Without that test, the agent presents the table and stops. Descriptive phrasing is also a claim: "largely/mostly mutually exclusive", "rarely co-occur", "tend to co-occur" are forbidden without the test — point to cBioPortal's Mutual Exclusivity tab instead. 3. **Never report a "median" that came from `AVG(...)` or any non-median aggregate.** "Median" and "mean" are different statistics; for skewed clinical distributions (especially survival) they differ substantially. Use ClickHouse's `quantile(0.5)(...)` for actual median, and label arithmetic averages as "mean", never "median". 4. **Never report a hazard ratio, odds ratio, risk ratio, or relative risk** that wasn't computed by an external tool. These require regression / model fitting that ClickHouse does not do. 5. **Never report median overall survival from `AVG(OS_MONTHS)` or even `quantile(0.5)(OS_MONTHS)`.** Median OS requires Kaplan-Meier estimation, which handles censoring (`OS_STATUS = 0:LIVING` means the event hasn't happened yet). Naive medians/means over `OS_MONTHS` ignore censoring and are systematically wrong. The correct handoff: return the raw `(OS_MONTHS, OS_STATUS)` pairs (or descriptive counts: N events, N censored, follow-up range) and tell the user to run KM in R (`survival::survfit`) or Python (`lifelines.KaplanMeierFitter`), or use cBioPortal's Survival comparison. If asked to do any of (1)–(5), respond with the appropriate handoff template from the "Approved Response Templates" section below — do not produce the number. Ambiguous-Term Clarification (before any analysis) -------------------------------------------------- If the user's question uses an ambiguous term, ask before computing anything. Examples: - **"aggressive"** → could mean shorter overall survival, higher metastasis rate, higher grade/stage, higher TMB, or specific molecular features. Ask which definit … (9984 more chars) ◀ result {"result":[{"cancer_study_identifier":"crc_eo_2020","name":"Colorectal Cancer (MSK, JNCI 2021)","type_of_cancer_id":"bowel","sample_count":1516,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_eo_2020"},{"cancer_study_identifier":"crc_msk_2017","name":"Metastatic Colorectal Cancer (MSK, Cancer Cell 2018)","type_of_cancer_id":"coadread","sample_count":1134,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_msk_2017"},{"cancer_study_identifier":"crc_sysucc_2022","name":"Colorectal Cancer- ChangKang Project (SYSUCC, Nat Commun 2022)","type_of_cancer_id":"coadread","sample_count":1015,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_sysucc_2022"},{"cancer_study_identifier":"coadread_dfci_2016","name":"Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)","type_of_cancer_id":"coadread","sample_count":619,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=coadread_dfci_2016"},{"cancer_study_identifier":"crc_apc_impact_2020","name":"Colorectal Cancer (MSK, Gastroenterology 2020)","type_of_cancer_id":"coadread","sample_count":471,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_apc_impact_2020"},{"cancer_study_identifier":"coadread_tcga_pub","name":"Colorectal Adenocarcinoma (TCGA, Nature 2012)","type_of_cancer_id":"coadread","sample_count":276,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=coadread_tcga_pub"},{"cancer_study_identifier":"coadread_cass_2020","name":"Colorectal Cancer (CAS Shanghai, Cancer Cell 2020)","type_of_cancer_id":"coadread","sample_count":146,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=coadread_cass_2020"},{"cancer_study_identifier":"crc_hta8_htan_2024","name":"Colorectal Cancer (HTAN MSK, Nature 2025)","type_of_cancer_id":"coadread","sample_count":83,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_hta8_htan_2024"},{"cancer_study_identifier":"crc_nigerian_2020","name":"Disparities in metastatic colorectal cancer between Africans and Americans (MSK, 2020)","type_of_cancer_id":"coadread","sample_count":64,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_nigerian_2020"},{"cancer_study_identifier":"rectal_radiation_msk_2024","name":"Colorectal Cancer Radiation (MSK, 2024)","type_of_cancer_id":"read","sample_count":48,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=rectal_radiation_msk_2024"},{"cancer_study_identifier":"crc_dd_2022","name":"Colorectal Cancer (MSK, JCO Precis Oncol 2022)","type_of_cancer_id":"coadread","sample_count":47,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=crc_dd_2022"},{"cancer_study_identifier":"coadread_mskresistance_2022","name":"Colorectal Cancer (MSK, Cancer Discovery 2022)","type_of_cancer_id":"coadread","sample_count":22,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=coadread_mskresistance_2022"},{"cancer_study_identifier":"msk_met_2021 … (1196 more chars) ▶ clickhouse_list_table_columns { "table": "cancer_study" } ◀ result {"columns":[{"name":"cancer_study_id","type":"Int64","comment":"Internal numeric ID. Prefer cancer_study_identifier for queries as it is more readable and stable."},{"name":"cancer_study_identifier","type":"Nullable(String)","comment":"Stable string identifier for the study (e.g., \"msk_chord_2024\", \"brca_tcga\"). Use this for filtering, not cancer_study_id."},{"name":"type_of_cancer_id","type":"String"},{"name":"name","type":"String","comment":"Full descriptive name of the study (e.g., \"MSK-CHORD (MSK, Nature 2024)\")."},{"name":"description","type":"String"},{"name":"public","type":"Int32"},{"name":"pmid","type":"Nullable(String)"},{"name":"citation","type":"Nullable(String)"},{"name":"groups","type":"Nullable(String)"},{"name":"status","type":"Nullable(Int64)"},{"name":"import_date","type":"Nullable(DateTime64(6))"},{"name":"reference_genome_id","type":"Nullable(Int64)"},{"name":"sample_count","type":"UInt32","comment":"Samples in the study (members of _all), as shown in the portal study list. Precomputed daily at LLM-prep time."},{"name":"mutation_sample_count","type":"UInt32","comment":"Samples profiled for mutations (_sequenced) — portal \"Data type\" filter: \"Mutations\". 0 = no mutation data."},{"name":"cna_sample_count","type":"UInt32","comment":"Samples profiled for copy-number alterations (_cna) — \"CNA\". 0 = no CNA data."},{"name":"structural_variant_sample_count","type":"UInt32","comment":"Distinct samples with at least one structural variant (fusions etc.). 0 = none."},{"name":"rna_seq_sample_count","type":"UInt32","comment":"Samples with RNA-Seq expression (_rna_seq_v2_mrna) — \"RNA-Seq\"."},{"name":"mrna_microarray_sample_count","type":"UInt32","comment":"Samples with microarray mRNA expression (_mrna) — \"RNA (microarray)\"."},{"name":"mirna_sample_count","type":"UInt32","comment":"Samples with microRNA expression (_microrna) — \"miRNA\"."},{"name":"rppa_sample_count","type":"UInt32","comment":"Samples with RPPA protein levels (_rppa) — \"RPPA\"."},{"name":"mass_spectrometry_sample_count","type":"UInt32","comment":"Samples with mass-spectrometry protein quantification (_protein_quantification) — \"Protein Mass-Spectrometry\"."},{"name":"treatment_patient_count","type":"UInt32","comment":"PATIENTS (not samples) with treatment clinical events — \"Treatment\". 0 = no treatment data."},{"name":"resource_sample_counts","type":"Map(String, UInt32)","comment":"Samples with each linked resource, keyed by display name: imaging and pathology such as 'Slide Microscopy', 'Computed Tomography', 'Magnetic Resonance', 'H&E Slide', 'MxIF Image'. Query with mapKeys(resource_sample_counts) or resource_sample_counts['Slide Microscopy'] > 0."},{"name":"mrna_expression_sample_count","type":"UInt32","comment":"Samples in any mRNA expression profile (RNA-Seq, microarray, TPM, z-scores; from sample_profile). Use this for \"does the study have expression data\" — rna_seq_sample_count and mrna_m … (136 more chars) ▶ clickhouse_run_select_query { "query": "SELECT DISTINCT c.cancer_study_identifier, c.name, c.mrna_expression_sample_count, COUNT(DISTINCT CASE WHEN attribute_id IN ('OS_MONTHS', 'OS_STATUS') THEN sample_unique_id END) AS samples_with_survival FROM cancer_study c LEFT JOIN clinical_data_derived cd ON c.cancer_study_identifier = cd.cancer_study_identifier WHERE c.type_of_cancer_id = 'coadread' AND c.mrna_expression_sample_count > 0 GROUP BY c.cancer_study_identifier, c.name, c.mrna_expression_sample_count ORDER BY c.mrna_expression_sample_count DESC LIMIT 10", "max_rows": 20 } ◀ 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 table expression identifier `attribute_id` in scope SELECT DISTINCT c.cancer_study_identifier, c.name, c.mrna_expression_sample_count, COUNTDistinct(multiIf((attribute_id IN ('OS_MONTHS', 'OS_STATUS')), sample_unique_id, NULL)) AS samples_with_survival FROM cancer_study AS c LEFT JOIN clinical_data_derived AS cd ON c.cancer_study_identifier = cd.cancer_study_identifier WHERE (c.type_of_cancer_id = 'coadread') AND (c.mrna_expression_sample_count > 0) GROUP BY c.cancer_study_identifier, c.name, c.mrna_expression_sample_count ORDER BY c.mrna_expression_sample_count DESC LIMIT 10. Maybe you meant: ['attribute_name']. (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 DISTINCT cancer_study_identifier FROM clinical_data_derived WHERE cancer_study_identifier IN ('coadread_tcga_pub', 'crc_msk_2017', 'crc_eo_2020') AND attribute_name IN ('OS_MONTHS', 'OS_STATUS') ORDER BY cancer_study_identifier", "max_rows": 20 } ◀ result {"rows":[{"cancer_study_identifier":"coadread_tcga_pub"},{"cancer_study_identifier":"crc_msk_2017"}]} ▶ clickhouse_run_select_query { "query": "SELECT DISTINCT cancer_study_identifier, molecular_profile_id FROM expression_derived WHERE cancer_study_identifier IN ('coadread_tcga_pub', 'crc_msk_2017') AND hugo_gene_symbol = 'IMPDH2' LIMIT 10", "max_rows": 20 } ◀ result {"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 60\n Code: 60. DB::Exception: Unknown table expression identifier 'expression_derived' in scope SELECT DISTINCT cancer_study_identifier, molecular_profile_id FROM expression_derived WHERE (cancer_study_identifier IN ('coadread_tcga_pub', 'crc_msk_2017')) AND (hugo_gene_symbol = 'IMPDH2') LIMIT 10. (UNKNOWN_TABLE) (version 26.4.1.2359 (official build))\n"} ▶ 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"}]} ▶ clickhouse_list_table_columns { "table": "genetic_alteration_derived" } ◀ result {"columns":[{"name":"sample_unique_id","type":"String"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"hugo_gene_symbol","type":"String"},{"name":"profile_type","type":"LowCardinality(String)"},{"name":"alteration_value","type":"Nullable(String)"}]} ▶ clickhouse_run_select_query { "query": "SELECT DISTINCT cancer_study_identifier, genetic_profile_id, alteration_type FROM genetic_alteration_derived WHERE cancer_study_identifier IN ('coadread_tcga_pub', 'crc_msk_2017') AND alteration_type LIKE '%mrna%' LIMIT 5", "max_rows": 20 } ◀ 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 `genetic_profile_id` in scope SELECT DISTINCT cancer_study_identifier, genetic_profile_id, alteration_type FROM genetic_alteration_derived WHERE (cancer_study_identifier IN ('coadread_tcga_pub', 'crc_msk_2017')) AND (alteration_type LIKE '%mrna%') LIMIT 5. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_run_select_query { "query": "SELECT DISTINCT cancer_study_identifier, profile_type, COUNT(DISTINCT sample_unique_id) as samples_with_data FROM genetic_alteration_derived WHERE hugo_gene_symbol = 'IMPDH2' AND cancer_study_identifier IN ('coadread_tcga_pub', 'crc_msk_2017') GROUP BY cancer_study_identifier, profile_type", "max_rows": 20 } ◀ result {"rows":[{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"linear_CNA","samples_with_data":257},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"methylation_hm27","samples_with_data":236},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"gistic","samples_with_data":257},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"mrna_merged_median_Zscores","samples_with_data":224},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"rna_seq_mrna_median_all_sample_Zscores","samples_with_data":244},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"rna_seq_mrna_median_Zscores","samples_with_data":244},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"rna_seq_mrna","samples_with_data":244},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"mrna","samples_with_data":224},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"mrna_median_all_sample_Zscores","samples_with_data":224},{"cancer_study_identifier":"coadread_tcga_pub","profile_type":"mrna_median_Zscores","samples_with_data":224}]} ▶ clickhouse_run_select_query { "query": "-- Get IMPDH2 expression and survival data for TCGA colorectal cancer WITH impdh2_data AS ( SELECT patient_unique_id, sample_unique_id, cancer_study_identifier, alteration_value::Float64 as impdh2_expression FROM genetic_alteration_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND hugo_gene_symbol = 'IMPDH2' AND profile_type = 'rna_seq_mrna' AND alteration_value != '' ), survival_data AS ( SELECT patient_unique_id, cancer_study_identifier, MAX(CASE WHEN attribute_name = 'OS_MONTHS' THEN toFloat64OrNull(attribute_value) END) as os_months, MAX(CASE WHEN attribute_name = 'OS_STATUS' THEN attribute_value END) as os_status FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND attribute_name IN ('OS_MONTHS', 'OS_STATUS') AND attribute_value != '' GROUP BY patient_unique_id, cancer_study_identifier ), combined_data AS ( SELECT im.patient_unique_id, im.impdh2_expression, sd.os_months, sd.os_status, CASE WHEN im.impdh2_expression >= 0 THEN 'High IMPDH2' ELSE 'Low IMPDH2' END as expression_group FROM impdh2_data im JOIN survival_data sd ON im.patient_unique_id = sd.patient_unique_id WHERE sd.os_months IS NOT NULL AND sd.os_status IS NOT NULL ) SELECT expression_group, COUNT(DISTINCT patient_unique_id) as n_patients, COUNT(CASE WHEN os_status = '1:DECEASED' THEN patient_unique_id END) as n_events, COUNT(CASE WHEN os_status = '0:LIVING' THEN patient_unique_id END) as n_censored, ROUND(quantile(0.5)(os_months), 1) as median_os_months, ROUND(MIN(os_months), 1) as min_followup, ROUND(MAX(os_months), 1) as max_followup, ROUND(AVG(os_months), 1) as mean_followup FROM combined_data GROUP BY expression_group ORDER BY expression_group", "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 identifier `patient_unique_id` in scope impdh2_data AS im. Maybe you meant: ['sample_unique_id']. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_run_select_query { "query": "-- Check what patient ID field is available SELECT DISTINCT sample_unique_id, cancer_study_identifier FROM genetic_alteration_derived WHERE hugo_gene_symbol = 'IMPDH2' AND cancer_study_identifier = 'coadread_tcga_pub' LIMIT 5", "max_rows": 10 } ◀ result {"rows":[{"sample_unique_id":"coadread_tcga_pub_TCGA-A6-2670-01","cancer_study_identifier":"coadread_tcga_pub"},{"sample_unique_id":"coadread_tcga_pub_TCGA-A6-2671-01","cancer_study_identifier":"coadread_tcga_pub"},{"sample_unique_id":"coadread_tcga_pub_TCGA-A6-2672-01","cancer_study_identifier":"coadread_tcga_pub"},{"sample_unique_id":"coadread_tcga_pub_TCGA-A6-2674-01","cancer_study_identifier":"coadread_tcga_pub"},{"sample_unique_id":"coadread_tcga_pub_TCGA-A6-2676-01","cancer_study_identifier":"coadread_tcga_pub"}]} ▶ clickhouse_run_select_query { "query": "-- Get IMPDH2 expression and survival data for TCGA colorectal cancer WITH impdh2_samples AS ( SELECT sample_unique_id, cancer_study_identifier, toFloat64OrNull(alteration_value) as impdh2_expression FROM genetic_alteration_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND hugo_gene_symbol = 'IMPDH2' AND profile_type = 'rna_seq_mrna' AND alteration_value != '' ), sample_to_patient AS ( SELECT DISTINCT sample_unique_id, patient_unique_id, cancer_study_identifier FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' ), survival_data AS ( SELECT patient_unique_id, cancer_study_identifier, MAX(CASE WHEN attribute_name = 'OS_MONTHS' THEN toFloat64OrNull(attribute_value) END) as os_months, MAX(CASE WHEN attribute_name = 'OS_STATUS' THEN attribute_value END) as os_status FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND attribute_name IN ('OS_MONTHS', 'OS_STATUS') AND attribute_value != '' GROUP BY patient_unique_id, cancer_study_identifier ), combined_data AS ( SELECT sp.patient_unique_id, im.impdh2_expression, sd.os_months, sd.os_status, CASE WHEN im.impdh2_expression >= 0 THEN 'High IMPDH2' ELSE 'Low IMPDH2' END as expression_group FROM impdh2_samples im LEFT JOIN sample_to_patient sp ON im.sample_unique_id = sp.sample_unique_id LEFT JOIN survival_data sd ON sp.patient_unique_id = sd.patient_unique_id WHERE sd.os_months IS NOT NULL AND sd.os_status IS NOT NULL ) SELECT expression_group, COUNT(DISTINCT patient_unique_id) as n_patients, COUNT(CASE WHEN os_status = '1:DECEASED' THEN patient_unique_id END) as n_events, COUNT(CASE WHEN os_status = '0:LIVING' THEN patient_unique_id END) as n_censored, ROUND(quantile(0.5)(os_months), 1) as median_os_months, ROUND(MIN(os_months), 1) as min_followup, ROUND(MAX(os_months), 1) as max_followup FROM combined_data GROUP BY expression_group ORDER BY expression_group", "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 `patient_unique_id` in scope WITH impdh2_samples AS (SELECT sample_unique_id, cancer_study_identifier, toFloat64OrNull(alteration_value) AS impdh2_expression FROM genetic_alteration_derived WHERE (cancer_study_identifier = 'coadread_tcga_pub') AND (hugo_gene_symbol = 'IMPDH2') AND (profile_type = 'rna_seq_mrna') AND (alteration_value != '')), sample_to_patient AS (SELECT DISTINCT sample_unique_id, patient_unique_id, cancer_study_identifier FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub'), survival_data AS (SELECT patient_unique_id, cancer_study_identifier, MAX(multiIf(attribute_name = 'OS_MONTHS', toFloat64OrNull(attribute_value), NULL)) AS os_months, MAX(multiIf(attribute_name = 'OS_STATUS', attribute_value, NULL)) AS os_status FROM clinical_data_derived WHERE (cancer_study_identifier = 'coadread_tcga_pub') AND (attribute_name IN ('OS_MONTHS', 'OS_STATUS')) AND (attribute_value != '') GROUP BY patient_unique_id, cancer_study_identifier), combined_data AS (SELECT sp.patient_unique_id, im.impdh2_expression, sd.os_months, sd.os_status, multiIf(im.impdh2_expression >= 0, 'High IMPDH2', 'Low IMPDH2') AS expression_group FROM impdh2_samples AS im LEFT JOIN sample_to_patient AS sp ON im.sample_unique_id = sp.sample_unique_id LEFT JOIN survival_data AS sd ON sp.patient_unique_id = sd.patient_unique_id WHERE (sd.os_months IS NOT NULL) AND (sd.os_status IS NOT NULL)) SELECT expression_group, COUNTDistinct(patient_unique_id) AS n_patients, COUNT(multiIf(os_status = '1:DECEASED', patient_unique_id, NULL)) AS n_events, COUNT(multiIf(os_status = '0:LIVING', patient_unique_id, NULL)) AS n_censored, ROUND(quantile(0.5)(os_months), 1) AS median_os_months, ROUND(MIN(os_months), 1) AS min_followup, ROUND(MAX(os_months), 1) AS max_followup FROM combined_data GROUP BY expression_group ORDER BY expression_group ASC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_run_select_query { "query": "SELECT sample_unique_id, patient_unique_id, attribute_name, attribute_value FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' LIMIT 10", "max_rows": 20 } ◀ result {"rows":[{"patient_unique_id":"coadread_tcga_pub_TCGA-A6-2670","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Sigmoid Colon"},{"patient_unique_id":"coadread_tcga_pub_TCGA-A6-2677","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Cecum"},{"patient_unique_id":"coadread_tcga_pub_TCGA-AA-3524","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Sigmoid Colon"},{"patient_unique_id":"coadread_tcga_pub_TCGA-AA-3529","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Sigmoid Colon"},{"patient_unique_id":"coadread_tcga_pub_TCGA-AA-3532","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Sigmoid Colon"},{"patient_unique_id":"coadread_tcga_pub_TCGA-AA-3538","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Descending Colon"},{"patient_unique_id":"coadread_tcga_pub_TCGA-AA-3544","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Sigmoid Colon"},{"patient_unique_id":"coadread_tcga_pub_TCGA-AA-3552","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Cecum"},{"patient_unique_id":"coadread_tcga_pub_TCGA-AA-3553","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Sigmoid Colon"},{"patient_unique_id":"coadread_tcga_pub_TCGA-AA-3562","attribute_name":"HISTOLOGICAL_SUBTYPE","attribute_value":"Descending Colon"}]} ▶ clickhouse_run_select_query { "query": "-- Get IMPDH2 expression and survival data - simplified approach WITH impdh2_samples AS ( SELECT sample_unique_id, cancer_study_identifier, toFloat64OrNull(alteration_value) as impdh2_expression FROM genetic_alteration_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND hugo_gene_symbol = 'IMPDH2' AND profile_type = 'rna_seq_mrna' AND alteration_value != '' ), patient_ids AS ( SELECT DISTINCT sample_unique_id, patient_unique_id FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' ), survival_data AS ( SELECT patient_unique_id, MAX(CASE WHEN attribute_name = 'OS_MONTHS' THEN toFloat64OrNull(attribute_value) END) as os_months, MAX(CASE WHEN attribute_name = 'OS_STATUS' THEN attribute_value END) as os_status FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND attribute_name IN ('OS_MONTHS', 'OS_STATUS') GROUP BY patient_unique_id ) SELECT CASE WHEN impdh2_expression >= 0 THEN 'High IMPDH2' ELSE 'Low IMPDH2' END as expression_group, COUNT(DISTINCT p.patient_unique_id) as n_patients, COUNT(DISTINCT CASE WHEN os_status = '1:DECEASED' THEN p.patient_unique_id END) as n_events, COUNT(DISTINCT CASE WHEN os_status = '0:LIVING' THEN p.patient_unique_id END) as n_censored, MIN(os_months) as min_followup_months, MAX(os_months) as max_followup_months FROM impdh2_samples im LEFT JOIN patient_ids p ON im.sample_unique_id = p.sample_unique_id LEFT JOIN survival_data s ON p.patient_unique_id = s.patient_unique_id WHERE s.os_months IS NOT NULL AND s.os_status IS NOT NULL GROUP BY expression_group ORDER BY expression_group", "max_rows": 100 } ◀ result {"rows":[{"expression_group":"High IMPDH2","n_patients":242,"n_events":23,"n_censored":219,"min_followup_months":0,"max_followup_months":72.01}]} ▶ clickhouse_run_select_query { "query": "-- Calculate median IMPDH2 expression first SELECT quantile(0.5)(toFloat64OrNull(alteration_value)) as median_expression FROM genetic_alteration_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND hugo_gene_symbol = 'IMPDH2' AND profile_type = 'rna_seq_mrna' AND alteration_value != ''", "max_rows": 10 } ◀ result {"rows":[{"median_expression":159.41525000000001}]} ▶ clickhouse_run_select_query { "query": "-- Get IMPDH2 expression and survival data stratified by median WITH impdh2_samples AS ( SELECT sample_unique_id, cancer_study_identifier, toFloat64OrNull(alteration_value) as impdh2_expression FROM genetic_alteration_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND hugo_gene_symbol = 'IMPDH2' AND profile_type = 'rna_seq_mrna' AND alteration_value != '' ), patient_ids AS ( SELECT DISTINCT sample_unique_id, patient_unique_id FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' ), survival_data AS ( SELECT patient_unique_id, MAX(CASE WHEN attribute_name = 'OS_MONTHS' THEN toFloat64OrNull(attribute_value) END) as os_months, MAX(CASE WHEN attribute_name = 'OS_STATUS' THEN attribute_value END) as os_status FROM clinical_data_derived WHERE cancer_study_identifier = 'coadread_tcga_pub' AND attribute_name IN ('OS_MONTHS', 'OS_STATUS') GROUP BY patient_unique_id ), combined_data AS ( SELECT p.patient_unique_id, im.impdh2_expression, s.os_months, s.os_status, CASE WHEN impdh2_expression >= 159.42 THEN 'High IMPDH2 (≥median)' ELSE 'Low IMPDH2 (= 159.42, 'High IMPDH2 (≥median)', 'Low IMPDH2 (= 159.42 THEN 'High IMPDH2' ELSE 'Low IMPDH2' END as expression_group, COUNT(DISTINCT c.patient_unique_id) as n_patients, COUNT(DISTINCT CASE WHEN c.attribute_name = 'OS_STATUS' AND c.attribute_value = '1:DECEASED' THEN c.patient_unique_id END) as n_events, COUNT(DISTINCT CASE WHEN c.attribute_name = 'OS_STATUS' AND c.attribute_value = '0:LIVING' THEN c.patient_unique_id END) as n_censored FROM genetic_alteration_derived g INNER JOIN clinical_data_derived c ON g.sample_unique_id = c.sample_unique_id AND g.cancer_study_identifier = c.cancer_study_identifier WHERE g.cancer_study_identifier = 'coadread_tcga_pub' AND g.hugo_gene_symbol = 'IMPDH2' AND g.profile_type = 'rna_seq_mrna' AND g.alteration_value != '' AND c.attribute_name IN ('OS_MONTHS', 'OS_STATUS') AND c.attribute_value != '' AND EXISTS ( SELECT 1 FROM clinical_data_derived c2 WHERE c2.patient_unique_id = c.patient_unique_id AND c2.attribute_name = 'OS_MONTHS' AND c2.attribute_value != '' ) GROUP BY expression_group ORDER BY expression_group 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 1\n Code: 1. DB::Exception: Resolved identifier 'c.patient_unique_id' in parent scope to expression 'c.patient_unique_id' with correlated columns 'patient_unique_id' (Enable 'allow_experimental_correlated_subqueries' setting to allow correlated subqueries execution). In scope (SELECT _CAST(1, 'UInt64') FROM (SELECT 1 FROM cbioportal_public_librechat_blue.clinical_data_derived AS c2 WHERE (c2.patient_unique_id = c.patient_unique_id) AND (c2.attribute_name = 'OS_MONTHS') AND (c2.attribute_value != '')) LIMIT _CAST(1, 'UInt64')). (UNSUPPORTED_METHOD) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_run_select_query { "query": "-- Get both IMPDH2 expression and OS status for each patient SELECT CASE WHEN toFloat64OrNull(g.alteration_value) >= 159.42 THEN 'High IMPDH2' ELSE 'Low IMPDH2' END as expression_group, c.attribute_name, c.attribute_value FROM genetic_alteration_derived g INNER JOIN clinical_data_derived c ON g.sample_unique_id = c.sample_unique_id WHERE g.cancer_study_identifier = 'coadread_tcga_pub' AND g.hugo_gene_symbol = 'IMPDH2' AND g.profile_type = 'rna_seq_mrna' AND g.alteration_value != '' AND c.attribute_name IN ('OS_MONTHS', 'OS_STATUS') AND c.attribute_value != '' LIMIT 100", "max_rows": 150 } ◀ result {"rows":[]} ▶ clickhouse_list_table_columns { "table": "sample_derived" } ◀ result {"columns":[{"name":"sample_unique_id","type":"String"},{"name":"sample_unique_id_base64","type":"String"},{"name":"sample_stable_id","type":"String"},{"name":"patient_unique_id","type":"String"},{"name":"patient_unique_id_base64","type":"String"},{"name":"patient_stable_id","type":"String"},{"name":"cancer_study_identifier","type":"LowCardinality(String)"},{"name":"internal_id","type":"Int32"},{"name":"patient_internal_id","type":"Int32"},{"name":"sample_type","type":"String"},{"name":"sequenced","type":"Int32"},{"name":"copy_number_segment_present","type":"Int32"}]} ▶ clickhouse_run_select_query { "query": "-- Get IMPDH2 expression and survival data using sample_derived SELECT CASE WHEN toFloat64OrNull(g.alteration_value) >= 159.42 THEN 'High IMPDH2 (≥median)' ELSE 'Low IMPDH2 (= 159.42 THEN 'High IMPDH2 (≥median)' ELSE 'Low IMPDH2 (= 159.42 THEN 'High IMPDH2 (≥median)' ELSE 'Low IMPDH2 (= 159.42, 'High IMPDH2 (≥median)', 'Low IMPDH2 (= 159.42 THEN 'High IMPDH2 (≥median)' ELSE 'Low IMPDH2 (= 159.42, 'High IMPDH2 (≥median)', 'Low IMPDH2 (= 159.42 THEN 'High IMPDH2 (≥median)' ELSE 'Low IMPDH2 (= 159.42 THEN 'High IMPDH2 (≥median)' ELSE 'Low IMPDH2 (