Fill the textbox with actualised* gene symbol (at least 2 characters must be entered)
and a dropdown list will appear, you can then select the gene you want to test.
If "gene symbol / all platforms" option is checked only gene symbols are shown in list.
If "gene symbol / Affymetrix platform" is checked only gene symbols represented by a probeset are listed.
Each probeset can be selected, if there is more than one probeset, three additional options are available:
Median probe: median value of all probesets corresponding to the selected gene is taken,
Highest probe: the probeset having the highest expression level is retained for the analysis (highest median value in a majority of U133P2 and U133A datasets;
in case of ties, decision was based on the total number of patients in the cohorts.),
JetSet probe: probeset with the highest score given by
Choose the kind of discretisation used for survival analyses as a splitting criterion:
"optimal": gene or probeset is split according to all percentiles from the 20th to the 80th, with a step of 5,
and the cutoff giving the best p-value (Cox model) is kept,
"customised percentile": choose any percentile from the 20th to the 80th, with a step of 1, to dichotomise the gene.
Once the 3 criteria have been chosen, click on "Submit".
After submission, a validation page shows information about the gene tested
and indicates number of patients and number of events in each subtype, before and after filtering, for the molecular subtyping method(s) chosen.
After visualising the validation screen, you can decide to validate or cancel your submission.
"Start analysis" will launch
with the chosen gene and direct you to molecular subtype prognostic analysis result page.
"Cancel" will redirect you back to previous screen, and offer you to choose a new gene.
Results are presented in one or 2 tables, depending on the number of subtyping methods chosen, summarizing analysis results
(Cox p-values and hazard ratios with 95% confidence interval, expression level for patients with good prognosis,
number of patients and events) for each molecular subtype.
Links to Kaplan-Meier curves are embedded in the table.
Gene results are displayed for each subtype defined by each predictor of the molecular subtyping method(s) chosen.
This analysis permits to evaluate the prognostic informativity of the gene per molecular subtype.
curve associated with the molecular subtype predictor can be visualise by clicking on one of the links embedded in the table:
"PNG" (for immediate and simple use) or "EMF" (to adjust the figure in accordance with the requirements of your article's publisher).