Affy ID/Gene symbol required.
INFO

Use multiple genes

Use list of genes Use mean expression of selected genes
Use ratio of two genes Filter by median expression
more genes param

Example

Example input for multiple genes:
1007_s_at 1
200000_s_at -1
31637_s_at 0.5
40016_g_at -2

Explanation:
first: normal,
second: gene is inverted,
third: gene has weight,
fourth: gene has weight and is inverted

You can also use following format:
1007_s_at, 1
200000_s_at, -1
31637_s_at, 0.5
40016_g_at, -2

Split patients by
Auto select best cutoff INFO
Trichotomization INFO
Survival: INFO Compute median survival: INFO
Follow up threshold: INFO Censore at threshold: INFO

Probe set options

Use
user selected probe set
all probe sets per gene INFO
only JetSet best probe set INFO
Plot beeswarm graph of probe distribution: INFO

Restrict analysis to subtypes...

ER status - IHC: (n=5667)
ER status - array: (n=7535)
PR status - IHC: (n=3548)
HER2 status - array: (n=7535)
Subtype - StGallen: (n=7535) INFO
Subtype - PAM50: (n=7535)
Lymph node status: (n=4994)
Grade: (n=4429)
TP53 status: (n=660)
Pietenpol subtype: (n=2041)
Use following dataset for the analysis:

Restrict analysis to selected cohorts...

 INFO

Restrict analysis based on cellular content...

B-cells:
CD4+ memory T-cells:
CD8+ T-cells:
Macrophages:
Natural killer T-cells:
Regulatory T-cells:

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Please kindly cite following paper to support further development: Posta M, Gyorffy B: Pathway-level mutational signatures predict breast cancer outcomes and reveal therapeutic targets, Brit J Pharmacol, 2025

Note: the generated p value does not include correction for multiple hypothesis testing by default.

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