Exhaustive prognostic analysis permits to screen the prognostic impact of a gene or a specific Affymetrix® probeset ID
on all possible combinations of population.
You have 2 criteria to choose.
gene expression data
First choose the data source (All DNA microarrays, METABRIC, TCGA...), then fill the textbox with actualised* gene symbol (at least 2 characters must be entered)
Affymetrix® probeset ID.
A dropdown list will appear, you can then select the gene you want to test.
The list of available genes depends on the previously chosen data source,
if any option, except "Affymetrix®", is checked only gene symbols available with selected data are shown in list.
If "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
Each population event is assigned to one button, while clicking on it the corresponding results table will be displayed.
The buttons color meter shows the p-values codes colors, indicating the trend of your gene for the considering event.
Results are displayed in a table for all subgroups defined by different nodal, oestrogen receptor and progesterone receptor for the chosen event status.
ordered by p-value (smallest to largest). Each line 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 subgroup combination.
Significant results may be considered robust if more than 5 combinations
among the 27 give a significant result.
If there are only 5 combinations or less with a p-value<0.05,
one cannot exclude a false discovery problem. However, if more
than 5 combinations give a significant result, the risk of false positive
rapidly decreases (6 or more, p<0.03; 7 or more, p<0.007;
8 or more, p<0.002; 9 or more, p<0.001).
Filters can be added by the user to focus on one or more parameters: choose one variable in the dropdown list on the top of considered column to filter it.
Automatically, the rows of the table will be filtered and displayed as wanted. (row numbers will be recomputed, and ordered by p-value (smallest to largest))
The circular arrow (at the left of filter dropdown lists) reset all filters previously chosen.
In result table of exhaustive prognostic analysis, you can see a
plot by clicking on appropriate button of your choice (with the figure drawn)
and/or download the full definition file in "PNG" (for immediate and simple use) or
"EMF" (to adjust the figure in accordance with the requirements of your article's publisher)
for each population (Node or ER or PR status) criteria on corresponding line.
If a discretisation option that results in more than two groups is chosen (at the first step of the analysis),
a sub table containing "Detailed Cox results" for all pairwise comparisons can be viewed by clicking on the "Open" button
present in "Detailed Cox" column of the main table.
In this example, quartile splitting criterion was chosen and detailed Cox results are shown for the third case: