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Table 3 Breast Cancer Pathway Analysis Summary

From: GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles

Met.

Subtypes

# Pathways a

Up in class 1

Up in 2

% DE genes

GR

Basal vs. Lum. A

324 (362)

324 (357)

0 (5)

33 (61)

GS

Basal vs. Lum. A

26

26

0

33 (61)

GR

Lum B. vs. Lum. A

322 (369)

322 (369)

0 (0)

10 (32)

GS

Lum B. vs. Lum. A

62

57

5

10 (32)

GR

Basal vs. Lum. B

115 (227)

102 (193)

13 (34)

23 (53)

GS

Basal vs. Lum. B

1

1

0

23 (53)

  1. aFor GRAPE significance threshold is Bonferroni P below 0.01, threshold of nominal 0.01 P-value shown in parentheses. For GSEA significance threshold is FDR q-value below 0.25