Q (sonnet):
In TCGA colorectal cancer, do patients with high PTK2 expression have different survival from patients with low PTK2 expression?
In Colorectal Adenocarcinoma (TCGA, PanCancer Atlas), the Kaplan-Meier curves for patients with PTK2 mRNA above vs below the median look slightly apart, with the high-PTK2 group doing a little worse early on. You can build this comparison in cBioPortal by querying PTK2 with an expression threshold (e.g. `PTK2: EXP>0`) and opening the Comparison → Survival tab.
Continue this conversation: reply to the user's new message.
is the difference in survival significant?
▶ resolve_and_route
{
"studyKeywords": [
"TCGA",
"colorectal",
"pan_can_atlas"
]
}
◀ result
{"success":true,"message":"Found 1 study. Use the metadata to call the appropriate navigation tool(s).","data":{"totalCount":1,"studiesWithMetadata":[{"studyId":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":594,"studyViewUrl":"https://www.cbioportal.org/study?id=coadread_tcga_pan_can_atlas_2018","metadata":{"clinicalAttributeIds":["AGE","AJCC_PATHOLOGIC_TUMOR_STAGE","AJCC_STAGING_EDITION","ANEUPLOIDY_SCORE","BUFFA_HYPOXIA_SCORE","CANCER_TYPE","CANCER_TYPE_ACRONYM","CANCER_TYPE_DETAILED","DAYS_LAST_FOLLOWUP","DAYS_TO_BIRTH","DAYS_TO_INITIAL_PATHOLOGIC_DIAGNOSIS","DFS_MONTHS","DFS_STATUS","DSS_MONTHS","DSS_STATUS","ETHNICITY","FORM_COMPLETION_DATE","FRACTION_GENOME_ALTERED","GENETIC_ANCESTRY_LABEL","GRADE","HISTORY_NEOADJUVANT_TRTYN","ICD_10","ICD_O_3_HISTOLOGY","ICD_O_3_SITE","INFORMED_CONSENT_VERIFIED","IN_PANCANPATHWAYS_FREEZE","MSI_SCORE_MANTIS","MSI_SENSOR_SCORE","MUTATION_COUNT","NEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT","ONCOTREE_CODE","OS_MONTHS","OS_STATUS","OTHER_PATIENT_ID","PATH_M_STAGE","PATH_N_STAGE","PATH_T_STAGE","PERSON_NEOPLASM_CANCER_STATUS","PFS_MONTHS","PFS_STATUS","PRIMARY_LYMPH_NODE_PRESENTATION_ASSESSMENT","PRIOR_DX","RACE","RADIATION_THERAPY","RAGNUM_HYPOXIA_SCORE","SAMPLE_COUNT","SAMPLE_TYPE","SEX","SOMATIC_STATUS","SUBTYPE","TBL_SCORE","TISSUE_PROSPECTIVE_COLLECTION_INDICATOR","TISSUE_RETROSPECTIVE_COLLECTION_INDICATOR","TISSUE_SOURCE_SITE","TISSUE_SOURCE_SITE_CODE","TMB_NONSYNONYMOUS","TUMOR_TISSUE_SITE","TUMOR_TYPE","WEIGHT","WINTER_HYPOXIA_SCORE"],"molecularProfileIds":["coadread_tcga_pan_can_atlas_2018_gistic","coadread_tcga_pan_can_atlas_2018_log2CNA","coadread_tcga_pan_can_atlas_2018_mutations","coadread_tcga_pan_can_atlas_2018_protein_quantification","coadread_tcga_pan_can_atlas_2018_protein_quantification_zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores","coadread_tcga_pan_can_atlas_2018_rppa","coadread_tcga_pan_can_atlas_2018_rppa_Zscores","coadread_tcga_pan_can_atlas_2018_structural_variants"],"genericAssayProfiles":["coadread_tcga_pan_can_atlas_2018_armlevel_cna","coadread_tcga_pan_can_atlas_2018_genetic_ancestry","coadread_tcga_pan_can_atlas_2018_methylation_hm27_hm450_merge","coadread_tcga_pan_can_atlas_2018_methylation_hm450"],"heatmapProfileIds":["coadread_tcga_pan_can_atlas_2018_protein_quantification_zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_Zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_Zscores","coadread_tcga_pan_can_atlas_2018_rna_seq_v2_mrna_median_all_sample_ref_normal_Zscores","coadread_tcga_pan_can_atlas_2018_rppa_Zscores"],"availableComparisonTabs":["overlap","clinical","survival","alterations","mutations","mrna","protein","generic_assay_armlevel_c … (70 more chars)
▶ navigate_to_results_view
{
"studyIds": [
"coadread_tcga_pan_can_atlas_2018"
],
"genes": [
"PTK2: EXP>0"
],
"profileFilter": "rna_seq_v2_mrna_median_Zscores",
"tab": "comparison/survival"
}
◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/results/comparison/survival?cancer_study_list=coadread_tcga_pan_can_atlas_2018&gene_list=PTK2%3A+EXP%3E0&case_set_id=coadread_tcga_pan_can_atlas_2018_all&profileFilter=rna_seq_v2_mrna_median_Zscores","url":"https://www.cbioportal.org/results/comparison/survival?cancer_study_list=coadread_tcga_pan_can_atlas_2018&gene_list=PTK2%3A+EXP%3E0&case_set_id=coadread_tcga_pan_can_atlas_2018_all&profileFilter=rna_seq_v2_mrna_median_Zscores","data":{"studyIds":["coadread_tcga_pan_can_atlas_2018"],"studies":[{"studyId":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","sampleCount":594}],"genes":["PTK2"],"caseSetId":"coadread_tcga_pan_can_atlas_2018_all","pageDescription":"Kaplan-Meier survival analysis comparing groups defined by query genes."}}
═ answer (success)
[Compare survival: PTK2 z-score > 0 (high) vs. ≤ 0 (low) in Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/results/comparison/survival?cancer_study_list=coadread_tcga_pan_can_atlas_2018&gene_list=PTK2%3A+EXP%3E0&case_set_id=coadread_tcga_pan_can_atlas_2018_all&profileFilter=rna_seq_v2_mrna_median_Zscores)
This link splits the 594-sample cohort into two groups by PTK2 mRNA z-score (above 0 = high, ≤ 0 = low, using the median-centered RNA-Seq z-scores) and opens the Survival tab, which will display the Kaplan-Meier curves for overall survival along with the log-rank test p-value directly on the plot. You can also switch to disease-free/progression-free survival endpoints from the same tab, and adjust the expression cutoff if you'd rather split by median expression exactly or use a different threshold.