Q (haiku): Which studies have RNA expression for renal cancer?

▶ search_oncotree
{
 "search_term": "renal"
}

◀ result
{"result":[{"code":"CCRCC","name":"Renal Clear Cell Carcinoma","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > CCRCC"},{"code":"MRC","name":"Renal Medullary Carcinoma","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > MRC"},{"code":"MTSCC","name":"Renal Mucinous Tubular Spindle Cell Carcinoma","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > MTSCC"},{"code":"NCCRCC","name":"Renal Non-Clear Cell Carcinoma","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC"},{"code":"RAML","name":"Renal Angiomyolipoma","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > RAML"},{"code":"RCC","name":"Renal Cell Carcinoma","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC"},{"code":"RNET","name":"Renal Neuroendocrine Tumor","score":60,"mainType":"Renal Neuroendocrine Tumor","tissue":"Kidney","hierarchy":"KIDNEY > RNET"},{"code":"ROCY","name":"Renal Oncocytoma","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > ROCY"},{"code":"RSCC","name":"Renal Small Cell Carcinoma","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > RSCC"},{"code":"SCCRCC","name":"Renal Clear Cell Carcinoma with Sarcomatoid Features","score":60,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > CCRCC > SCCRCC"},{"code":"ADRENAL_GLAND","name":"Adrenal Gland","score":50,"mainType":"Adrenal Gland Cancer","tissue":"Adrenal Gland","hierarchy":"ADRENAL_GLAND"},{"code":"CCPRC","name":"Clear Cell Papillary Renal Cell Carcinoma","score":50,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > CCPRC"},{"code":"CDRCC","name":"Collecting Duct Renal Cell Carcinoma","score":50,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > CDRCC"},{"code":"CHRCC","name":"Chromophobe Renal Cell Carcinoma","score":50,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > CHRCC"},{"code":"FHRCC","name":"FH-Deficient Renal Cell Carcinoma","score":50,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > FHRCC"},{"code":"NRCC","name":"NUTM1 Renal Cell Carcinoma","score":50,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NRCC"},{"code":"PRCC","name":"Papillary Renal Cell Carcinoma","score":50,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > PRCC"},{"code":"SRCC","name":"Sarcomatoid Renal Cell Carcinoma","score":50,"mainType":"Renal Cell Carcinoma","tissue":"Kidney","hierarchy":"KIDNEY > RCC > NCCRCC > SRCC"},{"code":"TRCC","name":"Translocation-Associated Renal Cell Carcinoma","score":50,"mainType":"Renal Cell Carcinoma","tis … (675 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
  cs.cancer_study_identifier,
  cs.name,
  cs.description,
  COUNT(DISTINCT s.sample_id) as sample_count,
  GROUP_CONCAT(DISTINCT mp.genetic_alteration_type) as data_types
FROM cancer_study cs
JOIN study_sample ss ON cs.cancer_study_id = ss.cancer_study_id
JOIN sample s ON ss.sample_id = s.sample_id
JOIN molecular_profile mp ON cs.cancer_study_id = mp.cancer_study_id
WHERE cs.type_of_cancer IN ('RCC', 'CCRCC', 'NCCRCC', 'PRCC', 'CHRCC', 'MRC')
  AND mp.genetic_alteration_type IN ('MRNA_EXPRESSION', 'EXPRESSION')
GROUP BY cs.cancer_study_identifier, cs.name, cs.description
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 60\n Code: 60. DB::Exception: Unknown table expression identifier 'molecular_profile' in scope SELECT cs.cancer_study_identifier, cs.name, cs.description, COUNTDistinct(s.sample_id) AS sample_count, GROUP_CONCATDistinct(mp.genetic_alteration_type) AS data_types FROM cancer_study AS cs INNER JOIN study_sample AS ss ON cs.cancer_study_id = ss.cancer_study_id INNER JOIN sample AS s ON ss.sample_id = s.sample_id INNER JOIN molecular_profile AS mp ON cs.cancer_study_id = mp.cancer_study_id WHERE (cs.type_of_cancer IN ('RCC', 'CCRCC', 'NCCRCC', 'PRCC', 'CHRCC', 'MRC')) AND (mp.genetic_alteration_type IN ('MRNA_EXPRESSION', 'EXPRESSION')) GROUP BY cs.cancer_study_identifier, cs.name, cs.description ORDER BY sample_count DESC. (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_run_select_query
{
 "query": "
SELECT 
  cs.cancer_study_identifier,
  cs.name,
  COUNT(DISTINCT s.sample_id) as sample_count,
  GROUP_CONCAT(DISTINCT gp.genetic_alteration_type) as data_types
FROM cancer_study cs
JOIN sample_derived s ON cs.cancer_study_identifier = s.study_id
JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
WHERE cs.type_of_cancer IN ('RCC', 'CCRCC', 'NCCRCC', 'PRCC', 'CHRCC', 'MRC')
  AND (gp.genetic_alteration_type LIKE '%MRNA%' OR gp.genetic_alteration_type LIKE '%RNA%' OR gp.genetic_alteration_type = 'EXPRESSION')
GROUP BY cs.cancer_study_identifier, cs.name
ORDER BY sample_count DESC
",
 "max_rows": 50
}

◀ 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: Identifier 's.study_id' cannot be resolved from table with name s. In scope SELECT cs.cancer_study_identifier, cs.name, COUNTDistinct(s.sample_id) AS sample_count, GROUP_CONCATDistinct(gp.genetic_alteration_type) AS data_types FROM cancer_study AS cs INNER JOIN sample_derived AS s ON cs.cancer_study_identifier = s.study_id INNER JOIN genetic_profile AS gp ON cs.cancer_study_id = gp.cancer_study_id WHERE (cs.type_of_cancer IN ('RCC', 'CCRCC', 'NCCRCC', 'PRCC', 'CHRCC', 'MRC')) AND ((gp.genetic_alteration_type LIKE '%MRNA%') OR (gp.genetic_alteration_type LIKE '%RNA%') OR (gp.genetic_alteration_type = 'EXPRESSION')) GROUP BY cs.cancer_study_identifier, cs.name ORDER BY sample_count DESC. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_list_table_columns
{
 "table": "genetic_profile"
}

▶ clickhouse_list_table_columns
{
 "table": "sample_derived"
}

◀ 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_list_table_columns
{
 "table": "cancer_study"
}

◀ 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"}]}

◀ 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 <study>_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 (<study>_sequenced) — portal \"Data type\" filter: \"Mutations\". 0 = no mutation data."},{"name":"cna_sample_count","type":"UInt32","comment":"Samples profiled for copy-number alterations (<study>_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 (<study>_rna_seq_v2_mrna) — \"RNA-Seq\"."},{"name":"mrna_microarray_sample_count","type":"UInt32","comment":"Samples with microarray mRNA expression (<study>_mrna) — \"RNA (microarray)\"."},{"name":"mirna_sample_count","type":"UInt32","comment":"Samples with microRNA expression (<study>_microrna) — \"miRNA\"."},{"name":"rppa_sample_count","type":"UInt32","comment":"Samples with RPPA protein levels (<study>_rppa) — \"RPPA\"."},{"name":"mass_spectrometry_sample_count","type":"UInt32","comment":"Samples with mass-spectrometry protein quantification (<study>_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 
  cancer_study_identifier,
  name,
  sample_count,
  rna_seq_sample_count,
  mrna_microarray_sample_count,
  mrna_expression_sample_count,
  (rna_seq_sample_count + mrna_microarray_sample_count) as total_rna_samples
FROM cancer_study
WHERE type_of_cancer_id IN ('RCC', 'CCRCC', 'NCCRCC', 'PRCC', 'CHRCC', 'MRC')
  AND (rna_seq_sample_count > 0 OR mrna_microarray_sample_count > 0)
ORDER BY mrna_expression_sample_count DESC, sample_count DESC
",
 "max_rows": 50
}

◀ result
{"rows":[]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT type_of_cancer_id
FROM cancer_study
WHERE type_of_cancer_id LIKE '%RCC%' OR type_of_cancer_id LIKE '%renal%' OR type_of_cancer_id = 'RCC'
ORDER BY type_of_cancer_id
",
 "max_rows": 50
}

◀ result
{"rows":[]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT type_of_cancer_id
FROM cancer_study
ORDER BY type_of_cancer_id
LIMIT 50
",
 "max_rows": 100
}

◀ result
{"rows":[{"type_of_cancer_id":"acbc"},{"type_of_cancer_id":"acc"},{"type_of_cancer_id":"acyc"},{"type_of_cancer_id":"adifg"},{"type_of_cancer_id":"alal"},{"type_of_cancer_id":"aml"},{"type_of_cancer_id":"ampca"},{"type_of_cancer_id":"angs"},{"type_of_cancer_id":"apad"},{"type_of_cancer_id":"bcc"},{"type_of_cancer_id":"bfn"},{"type_of_cancer_id":"biliary_tract"},{"type_of_cancer_id":"bladder"},{"type_of_cancer_id":"blca"},{"type_of_cancer_id":"bll"},{"type_of_cancer_id":"bowel"},{"type_of_cancer_id":"brain"},{"type_of_cancer_id":"brca"},{"type_of_cancer_id":"breast"},{"type_of_cancer_id":"ccrcc"},{"type_of_cancer_id":"cervix"},{"type_of_cancer_id":"cesc"},{"type_of_cancer_id":"chl"},{"type_of_cancer_id":"chol"},{"type_of_cancer_id":"chrcc"},{"type_of_cancer_id":"cllsll"},{"type_of_cancer_id":"coad"},{"type_of_cancer_id":"coadread"},{"type_of_cancer_id":"cscc"},{"type_of_cancer_id":"desm"},{"type_of_cancer_id":"difg"},{"type_of_cancer_id":"dlbclnos"},{"type_of_cancer_id":"egc"},{"type_of_cancer_id":"es"},{"type_of_cancer_id":"esca"},{"type_of_cancer_id":"escc"},{"type_of_cancer_id":"gbc"},{"type_of_cancer_id":"gist"},{"type_of_cancer_id":"hcc"},{"type_of_cancer_id":"hccihch"},{"type_of_cancer_id":"hdcn"},{"type_of_cancer_id":"head_neck"},{"type_of_cancer_id":"hgsoc"},{"type_of_cancer_id":"hnsc"},{"type_of_cancer_id":"ihch"},{"type_of_cancer_id":"lgsoc"},{"type_of_cancer_id":"liad"},{"type_of_cancer_id":"lipo"},{"type_of_cancer_id":"luad"},{"type_of_cancer_id":"lung"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT type_of_cancer_id
FROM cancer_study
WHERE type_of_cancer_id IN ('rcc', 'ccrcc', 'nccrcc', 'prcc', 'chrcc', 'mrc', 'urcc')
ORDER BY type_of_cancer_id
",
 "max_rows": 50
}

◀ result
{"rows":[{"type_of_cancer_id":"ccrcc"},{"type_of_cancer_id":"chrcc"},{"type_of_cancer_id":"nccrcc"},{"type_of_cancer_id":"prcc"},{"type_of_cancer_id":"rcc"},{"type_of_cancer_id":"urcc"}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT 
  cancer_study_identifier,
  name,
  sample_count,
  rna_seq_sample_count,
  mrna_microarray_sample_count,
  mrna_expression_sample_count
FROM cancer_study
WHERE type_of_cancer_id IN ('rcc', 'ccrcc', 'nccrcc', 'prcc', 'chrcc', 'mrc', 'urcc')
  AND mrna_expression_sample_count > 0
ORDER BY mrna_expression_sample_count DESC
",
 "max_rows": 50
}

◀ result
{"rows":[{"cancer_study_identifier":"kirc_tcga","name":"Kidney Renal Clear Cell Carcinoma (TCGA, Firehose Legacy)","sample_count":538,"rna_seq_sample_count":534,"mrna_microarray_sample_count":72,"mrna_expression_sample_count":535},{"cancer_study_identifier":"ccrcc_tcga_gdc","name":"Renal Clear Cell Carcinoma (TCGA GDC, 2025)","sample_count":537,"rna_seq_sample_count":0,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":534},{"cancer_study_identifier":"kirc_tcga_pan_can_atlas_2018","name":"Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)","sample_count":512,"rna_seq_sample_count":510,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":510},{"cancer_study_identifier":"kirc_tcga_pub","name":"Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)","sample_count":446,"rna_seq_sample_count":417,"mrna_microarray_sample_count":56,"mrna_expression_sample_count":426},{"cancer_study_identifier":"rcc_cptac_gdc","name":"Renal Cell Carcinoma (CPTAC GDC, 2025)","sample_count":354,"rna_seq_sample_count":0,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":353},{"cancer_study_identifier":"kirp_tcga","name":"Kidney Renal Papillary Cell Carcinoma (TCGA, Firehose Legacy)","sample_count":293,"rna_seq_sample_count":291,"mrna_microarray_sample_count":16,"mrna_expression_sample_count":291},{"cancer_study_identifier":"prcc_tcga_gdc","name":"Papillary Renal Cell Carcinoma (TCGA GDC, 2025)","sample_count":292,"rna_seq_sample_count":0,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":291},{"cancer_study_identifier":"kirp_tcga_pan_can_atlas_2018","name":"Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)","sample_count":283,"rna_seq_sample_count":283,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":283},{"cancer_study_identifier":"rcc_iatlas_immotion150_2018","name":"Renal Cell Carcinoma (IMmotion150 Clinical Trial, Nat Med. 2018) - iAtlas Harmonized","sample_count":263,"rna_seq_sample_count":0,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":263},{"cancer_study_identifier":"kich_tcga","name":"Kidney Chromophobe (TCGA, Firehose Legacy)","sample_count":113,"rna_seq_sample_count":66,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":66},{"cancer_study_identifier":"kich_tcga_pub","name":"Kidney Chromophobe (TCGA, Cancer Cell 2014)","sample_count":66,"rna_seq_sample_count":66,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":66},{"cancer_study_identifier":"chrcc_tcga_gdc","name":"Chromophobe Renal Cell Carcinoma (TCGA GDC, 2025)","sample_count":66,"rna_seq_sample_count":0,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":66},{"cancer_study_identifier":"kich_tcga_pan_can_atlas_2018","name":"Kidney Chromophobe (TCGA, PanCancer Atlas)","sample_count":65,"rna_seq_sample_count":65,"mrna_microarray_sample_count":0,"mrna_expression_sample_count":65},{"cancer_study_identifier":"ccrcc_iatlas_choueiri_2016","name":"Metastatic Renal Clear Cell Carcin … (186 more chars)

═ answer (success)
Perfect! Here are the renal cancer studies with RNA expression data:

## Renal Cancer Studies with RNA Expression

**14 studies** have RNA expression data for renal cancer:

| Study ID | Study Name | Total Samples | RNA-Seq | Microarray | Total RNA Samples |
|-----------|-----------|---------------|---------|-----------|-------------------|
| **kirc_tcga** | Kidney Renal Clear Cell Carcinoma (TCGA, Firehose Legacy) | 538 | 534 | 72 | 535 |
| **ccrcc_tcga_gdc** | Renal Clear Cell Carcinoma (TCGA GDC, 2025) | 537 | — | — | 534 |
| **kirc_tcga_pan_can_atlas_2018** | Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas) | 512 | 510 | — | 510 |
| **kirc_tcga_pub** | Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013) | 446 | 417 | 56 | 426 |
| **rcc_cptac_gdc** | Renal Cell Carcinoma (CPTAC GDC, 2025) | 354 | — | — | 353 |
| **kirp_tcga** | Kidney Renal Papillary Cell Carcinoma (TCGA, Firehose Legacy) | 293 | 291 | 16 | 291 |
| **prcc_tcga_gdc** | Papillary Renal Cell Carcinoma (TCGA GDC, 2025) | 292 | — | — | 291 |
| **kirp_tcga_pan_can_atlas_2018** | Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas) | 283 | 283 | — | 283 |
| **rcc_iatlas_immotion150_2018** | Renal Cell Carcinoma (IMmotion150 Clinical Trial, Nat Med. 2018) - iAtlas Harmonized | 263 | — | — | 263 |
| **kich_tcga** | Kidney Chromophobe (TCGA, Firehose Legacy) | 113 | 66 | — | 66 |
| **kich_tcga_pub** | Kidney Chromophobe (TCGA, Cancer Cell 2014) | 66 | 66 | — | 66 |
| **chrcc_tcga_gdc** | Chromophobe Renal Cell Carcinoma (TCGA GDC, 2025) | 66 | — | — | 66 |
| **kich_tcga_pan_can_atlas_2018** | Kidney Chromophobe (TCGA, PanCancer Atlas) | 65 | 65 | — | 65 |
| **ccrcc_iatlas_choueiri_2016** | Metastatic Renal Clear Cell Carcinoma (Phase 1 Biomarker Trial, Clin Cancer Res. 2016) - iAtlas Harmonized | 16 | — | — | 16 |

**Top recommendations:**
- **kirc_tcga_pan_can_atlas_2018** — 510 RNA-Seq samples from the PanCancer Atlas (recommended for most analyses)
- **ccrcc_tcga_gdc** — 534 samples, latest 2025 GDC harmonization
- **kirc_tcga** — 535 total RNA samples (mix of sequencing methods)