Q (sonnet): <conversation_so_far>
<user>
In TCGA colorectal cancer, do patients with high PTK2 expression have different survival from patients with low PTK2 expression?
</user>

<assistant>
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.
</assistant>
</conversation_so_far>

Continue this conversation: reply to the user's new message.

<user>
is the difference in survival significant?
</user>

▶ resolve_and_route
{
 "studyKeywords": [
  "colorectal",
  "TCGA",
  "pan_can_atlas"
 ]
}

◀ result
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▶ navigate_to_group_comparison
{
 "studyIds": [
  "coadread_tcga_pan_can_atlas_2018"
 ],
 "groups": [
  {
   "name": "PTK2 High",
   "studyViewFilter": {
    "genomicDataFilters": [
     {
      "hugoGeneSymbol": "PTK2",
      "profileType": "rna_seq_v2_mrna_median_all_sample_Zscores",
      "values": [
       {
        "start": 0
       }
      ]
     }
    ]
   }
  },
  {
   "name": "PTK2 Low",
   "studyViewFilter": {
    "genomicDataFilters": [
     {
      "hugoGeneSymbol": "PTK2",
      "profileType": "rna_seq_v2_mrna_median_all_sample_Zscores",
      "values": [
       {
        "end": 0
       }
      ]
     }
    ]
   }
  }
 ],
 "tab": "survival"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/comparison/survival?comparisonId=6ab82241c2115c492d885167","url":"https://www.cbioportal.org/comparison/survival?comparisonId=6ab82241c2115c492d885167","data":{"description":"Group comparison (2 custom groups)","studies":["coadread_tcga_pan_can_atlas_2018"],"totalGroups":2,"groups":[{"name":"PTK2 High","sampleCount":295},{"name":"PTK2 Low","sampleCount":297}],"studyViewUrl":"https://www.cbioportal.org/study?id=coadread_tcga_pan_can_atlas_2018","groupUrls":[{"groupName":"PTK2 High","url":"https://www.cbioportal.org/study?id=coadread_tcga_pan_can_atlas_2018#filterJson=%7B%22genomicDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22PTK2%22%2C%22profileType%22%3A%22rna_seq_v2_mrna_median_all_sample_Zscores%22%2C%22values%22%3A%5B%7B%22start%22%3A0%7D%5D%7D%5D%7D"},{"groupName":"PTK2 Low","url":"https://www.cbioportal.org/study?id=coadread_tcga_pan_can_atlas_2018#filterJson=%7B%22genomicDataFilters%22%3A%5B%7B%22hugoGeneSymbol%22%3A%22PTK2%22%2C%22profileType%22%3A%22rna_seq_v2_mrna_median_all_sample_Zscores%22%2C%22values%22%3A%5B%7B%22end%22%3A0%7D%5D%7D%5D%7D"}],"pageDescription":"Kaplan-Meier survival analysis comparing PTK2 High (295) vs PTK2 Low (297)."}}

═ answer (success)
I've set up the formal comparison for you in **Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)**:

- **PTK2 High** (z-score ≥ 0): 295 samples
- **PTK2 Low** (z-score < 0): 297 samples

[View PTK2 High vs Low — Survival Comparison](https://www.cbioportal.org/comparison/survival?comparisonId=6ab82241c2115c492d885167)

Opening this link will show the Kaplan-Meier curves for overall survival (and other endpoints, like disease-free survival, if you switch the outcome selector) along with the **log-rank p-value** computed directly on the page — that's the proper significance test for this comparison, and I'd rather point you to it than guess at a number.

A couple of notes on interpreting it once you're there:
- Check the number of events (deaths) in each group, not just sample size — if events are sparse, the median survival line may show "not reached," which limits how confident you can be in any p-value.
- If you want a different split point (e.g., quartiles instead of median z-score) rather than an above/below-zero z-score cutoff, let me know and I can rebuild the groups.