What is the KM plotter?
The KM plotter is capable to assess the effect of 22,277 genes on survival in 2,472 breast cancer and 1,287 ovarian cancer patients. The primary purpose of the tool is a meta-analysis based in silico biomarker assessment.
How does it work?
A background database was established using gene expression data and survival information downloaded from GEO (Affymetrix HGU133A and HGU133+2 microarrays). After quality control and normalization only probes present on both Affymetrix platforms are retained (n=22,277). The background database is handled by a PostgreSQL server, which integrates gene expression and clinical data simultaneously. To analyze the prognostic value of a particular gene, the patient samples are split into two groups according to various quantile expressions of the proposed biomarker. The two patient cohorts can be compared in terms of relapse free survival or overall survival. A survival curve is displayed, and the hazard ratio with 95% confidence intervals and logrank P value are calculated and displayed.
Is this some sort of database?
No! The KM plotter performs the computation in real time on our server. This can result in slow response when using multiple probe sets simultaneously. Please be patient when waiting for the results.
Which gene ID can I use?
KM-plot recognizes 22,277 Affymetrix probe set IDs and 70,632 gene symbols (this includes the HUGO Gene Nomenclature Committee (EMBL Hinxton) approved official gene symbols, previously used gene symbols and aliases).
Can I use multiple genes?
Yes. Click on the button "Enter more Affy IDs" and enter multiple Affymetrix IDs. You can run the analysis on all these biomarkers simultaneously (default setting), or using the mean expression of the genes. For this, tick the "Use mean expression of the selected probes" box.
I have several candidates. Which biomarker is the most significant?
To correct for multiple testing, please use our multiple testing calculator.
Want to predict survival for a single patient?
Try Recurrence Online, a tool capable to predict response to hormonal treatment, to targeted therapy and survival (recurrence score) for breast cancer patients using gene expression data obtained by Affymetrix microarrays.
Do you want to know more?
For further technical details and sample biomarker validation please see our manuscripts.
Breast cancer: Look it up in Google scholar.
Ovarian cancer: submitted for publication.
Version notice: Want to use the original version of the KM-plotter working with 1809 breast cancer patients? Click here.