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

▶ list_studies
{
 "search": "renal",
 "limit": "100",
 "verbose": "true"
}

✗ error
<tool_use_error>Error: No such tool available: mcp__navigator__list_studies</tool_use_error>

▶ list_studies
{
 "search": "renal",
 "limit": 100,
 "verbose": true
}

◀ result
{"result":[{"cancer_study_identifier":"ccrcc_sjuh_2023","name":"Renal Cell Carcinoma (St. James, Clin Cancer Res 2023)","description":"Targeted sequencing of 943 renal clear cell carcinoma samples and their matched normals.","type_of_cancer_id":"ccrcc","sample_count":943,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=ccrcc_sjuh_2023"},{"cancer_study_identifier":"kirc_tcga","name":"Kidney Renal Clear Cell Carcinoma (TCGA, Firehose Legacy)","description":"TCGA Kidney Renal Clear Cell Carcinoma. Source data from <A HREF=\"http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/KIRC/20160128/\">GDAC Firehose</A>. Previously known as TCGA Provisional.","type_of_cancer_id":"ccrcc","sample_count":538,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=kirc_tcga"},{"cancer_study_identifier":"ccrcc_tcga_gdc","name":"Renal Clear Cell Carcinoma (TCGA GDC, 2025)","description":"TCGA Renal Clear Cell Carcinoma. Source data from <A HREF=\"https://gdc.cancer.gov\">NCI GDC</A> and generated in Aug 2025 using <A HREF=\"https://cda.readthedocs.io/en/latest/\">Cancer Data Aggregator</A>.","type_of_cancer_id":"ccrcc","sample_count":537,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=ccrcc_tcga_gdc"},{"cancer_study_identifier":"kirc_tcga_pan_can_atlas_2018","name":"Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)","description":"Kidney Renal Clear Cell Carcinoma TCGA PanCancer data. The original data is <a href=\"https://gdc.cancer.gov/about-data/publications/pancanatlas\">here</a>. The publications are <a href=\"https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html\">here</a>.","type_of_cancer_id":"ccrcc","sample_count":512,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=kirc_tcga_pan_can_atlas_2018"},{"cancer_study_identifier":"kirc_tcga_pub","name":"Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)","description":"Whole-exome sequencing in 417 of 446 clear cell renal cell carcinoma tumor/normal pairs.","type_of_cancer_id":"ccrcc","sample_count":446,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=kirc_tcga_pub"},{"cancer_study_identifier":"rcc_cptac_gdc","name":"Renal Cell Carcinoma (CPTAC GDC, 2025)","description":"CPTAC Renal Cell Carcinoma. Source data from <A HREF=\"https://gdc.cancer.gov\">NCI GDC</A> and generated in Aug 2025 using <A HREF=\"https://cda.readthedocs.io/en/latest/\">Cancer Data Aggregator</A>.","type_of_cancer_id":"rcc","sample_count":354,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=rcc_cptac_gdc"},{"cancer_study_identifier":"kirp_tcga","name":"Kidney Renal Papillary Cell Carcinoma (TCGA, Firehose Legacy)","description":"TCGA Kidney Renal Papillary Cell Carcinoma. Source data from <A HREF=\"http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/KIRP/20160128/\">GDAC Firehose</A>. Previously known as TCGA Provisional.","type_of_cancer_id":"prcc","sample_count":293,"has_guide" … (5485 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT 
  cs.cancer_study_identifier,
  cs.name,
  mp.genetic_alteration_type,
  mp.datatype,
  mp.show_profile_in_analysis_tab
FROM cancer_study cs
JOIN genetic_profile mp ON cs.cancer_study_id = mp.cancer_study_id
WHERE cs.type_of_cancer_id IN ('ccrcc', 'prcc', 'rcc', 'nccrcc', 'chrcc', 'urcc')
  AND mp.genetic_alteration_type LIKE '%expression%'
ORDER BY cs.cancer_study_identifier, mp.genetic_alteration_type
",
 "max_rows": 200
}

◀ result
{"rows":[]}

▶ 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 
  cs.cancer_study_identifier,
  cs.name,
  gp.genetic_alteration_type,
  gp.datatype,
  gp.name as profile_name
FROM cancer_study cs
JOIN genetic_profile gp ON cs.cancer_study_id = gp.cancer_study_id
WHERE cs.type_of_cancer_id IN ('ccrcc', 'prcc', 'rcc', 'nccrcc', 'chrcc', 'urcc')
  AND (gp.genetic_alteration_type = 'MRNA_EXPRESSION' 
       OR gp.genetic_alteration_type = 'PROTEIN_LEVEL'
       OR gp.datatype = 'CONTINUOUS')
ORDER BY cs.cancer_study_identifier, gp.name
",
 "max_rows": 200
}

◀ result
{"rows":[{"cancer_study_identifier":"ccrcc_iatlas_choueiri_2016","name":"Metastatic Renal Clear Cell Carcinoma (Phase 1 Biomarker Trial, Clin Cancer Res. 2016) - iAtlas Harmonized","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"CONTINUOUS","profile_name":"mRNA expression (log2 upper quartile normalized counts)"},{"cancer_study_identifier":"ccrcc_iatlas_choueiri_2016","name":"Metastatic Renal Clear Cell Carcinoma (Phase 1 Biomarker Trial, Clin Cancer Res. 2016) - iAtlas Harmonized","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"Z-SCORE","profile_name":"mRNA expression z-scores (log2 upper quartile normalized counts)"},{"cancer_study_identifier":"ccrcc_tcga_gdc","name":"Renal Clear Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"CONTINUOUS","profile_name":"mRNA Expression"},{"cancer_study_identifier":"ccrcc_tcga_gdc","name":"Renal Clear Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"CONTINUOUS","profile_name":"mRNA Expression (FPKM)"},{"cancer_study_identifier":"ccrcc_tcga_gdc","name":"Renal Clear Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"CONTINUOUS","profile_name":"mRNA Expression (TPM)"},{"cancer_study_identifier":"ccrcc_tcga_gdc","name":"Renal Clear Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"Z-SCORE","profile_name":"mRNA Expression FPKM z-scores"},{"cancer_study_identifier":"ccrcc_tcga_gdc","name":"Renal Clear Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"Z-SCORE","profile_name":"mRNA Expression TPM z-scores"},{"cancer_study_identifier":"ccrcc_tcga_gdc","name":"Renal Clear Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"Z-SCORE","profile_name":"mRNA Expression z-scores"},{"cancer_study_identifier":"chrcc_tcga_gdc","name":"Chromophobe Renal Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"CONTINUOUS","profile_name":"mRNA Expression"},{"cancer_study_identifier":"chrcc_tcga_gdc","name":"Chromophobe Renal Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"CONTINUOUS","profile_name":"mRNA Expression (FPKM)"},{"cancer_study_identifier":"chrcc_tcga_gdc","name":"Chromophobe Renal Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"CONTINUOUS","profile_name":"mRNA Expression (TPM)"},{"cancer_study_identifier":"chrcc_tcga_gdc","name":"Chromophobe Renal Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"Z-SCORE","profile_name":"mRNA Expression FPKM z-scores"},{"cancer_study_identifier":"chrcc_tcga_gdc","name":"Chromophobe Renal Cell Carcinoma (TCGA GDC, 2025)","genetic_alteration_type":"MRNA_EXPRESSION","datatype":"Z-SCORE","profile_name":"mRNA Expression TPM z-scores"},{"cancer_study_identifier":"chrcc_tcga_gdc","name":"Chromophobe  … (18735 more chars)

═ answer (success)
## Renal Cancer Studies with RNA Expression Data

The following **8 renal cancer studies** have RNA expression (mRNA) data available:

### Clear Cell RCC
1. **[Renal Clear Cell Carcinoma (TCGA GDC, 2025)](https://www.cbioportal.org/study/summary?id=ccrcc_tcga_gdc)** — 537 samples
   - mRNA Expression (FPKM, TPM, counts) with z-scores

2. **[Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=kirc_tcga_pan_can_atlas_2018)** — 512 samples
   - mRNA Expression RSEM with z-scores

3. **[Kidney Renal Clear Cell Carcinoma (TCGA, Firehose Legacy)](https://www.cbioportal.org/study/summary?id=kirc_tcga)** — 538 samples
   - mRNA Expression (RNA-Seq V2 RSEM + microarray) with z-scores

4. **[Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)](https://www.cbioportal.org/study/summary?id=kirc_tcga_pub)** — 446 samples
   - mRNA Expression (RNA-Seq V2 RSEM + microarray) plus miRNA expression

5. **[Metastatic Renal Clear Cell Carcinoma (Phase 1 Biomarker Trial, Clin Cancer Res. 2016) - iAtlas Harmonized](https://www.cbioportal.org/study/summary?id=ccrcc_iatlas_choueiri_2016)** — 16 samples
   - mRNA Expression (log2 upper quartile normalized) with z-scores

### Papillary RCC
6. **[Papillary Renal Cell Carcinoma (TCGA GDC, 2025)](https://www.cbioportal.org/study/summary?id=prcc_tcga_gdc)** — 292 samples
   - mRNA Expression (FPKM, TPM, counts) with z-scores

7. **[Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=kirp_tcga_pan_can_atlas_2018)** — 283 samples
   - mRNA Expression RSEM with z-scores

8. **[Kidney Renal Papillary Cell Carcinoma (TCGA, Firehose Legacy)](https://www.cbioportal.org/study/summary?id=kirp_tcga)** — 293 samples
   - mRNA Expression (RNA-Seq V2 RSEM + microarray) with z-scores

### Chromophobe RCC
9. **[Chromophobe Renal Cell Carcinoma (TCGA GDC, 2025)](https://www.cbioportal.org/study/summary?id=chrcc_tcga_gdc)** — 66 samples
   - mRNA Expression (FPKM, TPM, counts) with z-scores

10. **[Kidney Chromophobe (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=kich_tcga_pan_can_atlas_2018)** — 283 samples
    - mRNA Expression RSEM with z-scores

11. **[Kidney Chromophobe (TCGA, Firehose Legacy)](https://www.cbioportal.org/study/summary?id=kich_tcga)** — 293 samples
    - mRNA Expression (RNA-Seq V2 RSEM) with z-scores

### Clinical Trial RCC
12. **[Renal Cell Carcinoma (IMmotion150 Clinical Trial, Nat Med. 2018) - iAtlas Harmonized](https://www.cbioportal.org/study/summary?id=rcc_iatlas_immotion150_2018)** — 263 samples
    - mRNA Expression (TPM) with z-scores

13. **[Renal Cell Carcinoma (CPTAC GDC, 2025)](https://www.cbioportal.org/study/summary?id=rcc_cptac_gdc)** — 354 samples
    - mRNA Expression (FPKM, TPM, counts) with z-scores

**Note:** The TCGA 2025 GDC updates (ccrcc_tcga_gdc, prcc_tcga_gdc, chrcc_tcga_gdc, rcc_cptac_gdc) are the most current versions and are recommended for new analyses.