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Supplemental Data 
Contents:

Supplemental Figure 1: Hierarchical clustering of 115 breast tumor tissues and 7 non-malignant tissues using the "intrinsic" gene set.

Slightly enhanced version of Figure 1.

(Also available as Portable Document Format [PDF])


Supplemental Figure 2: Hierarchical clustering of gene expression data from van't Veer et al.

Slightly enhanced version of Figure 2.

(Also available as Portable Document Format [PDF])


Supplemental Figure 3: BRCA1 tumors associated with a basal tumor profile.

Slightly enhanced version of Figure 3.

(Also available as Portable Document Format [PDF])


Supplemental Figure 4: Hierarchical clustering of gene expression data from West et al.

Slightly enhanced version of Figure 4.

(Also available as Portable Document Format [PDF])


Supplemental Figure 5: Kaplan-Meier analysis of disease outcome in two patient cohorts.

Slightly enhanced version of Figure 5.

(Also available as Portable Document Format [PDF])


Supplemental Figure 6: The full cluster showing the expression patterns of 552 intrinsic clones (from the 561 intrinsic gene list) across 122 breast tissue samples from the Norway/Stanford data set.

(Also available as Portable Document Format [PDF])


Supplemental Figure 7: The full cluster diagram of the 97 sporadic tumors from van't Veer et al. using the 461 intrinsic genes (represented by 504 clones).

(Also available as Portable Document Format [PDF])


Supplemental Figure 8: The full cluster of the 117 breast tumors from van't Veer et al., including 18 BRCA1 carriers and two BRCA2 carriers, using expression data from the 461 the intrinsic genes.

(Also available as Portable Document Format [PDF])


Supplemental Figure 9: The complete cluster of the 49 primary breast tumor analyzed by West et al. using 242 of the intrinsic genes.

(Also available as Portable Document Format [PDF])


Supplemental Table 2: Complete data table containing all experimental samples. "Previously published" refers to Sørlie et al. PNAS 98, 10869-10874, 2001. A=alive; AWD=alive with disease; DOD=dead of disease; DOC=dead of other cause; na=not available.

Available as:

  1. MS Excel spreadsheet
  2. Tab-delimited Text File


Supplemental Table 3: Class prediction using Prediction Analysis of Microarrays: Consistency between hierarchical clustering and prediction for the three data sets.

Available as:

  1. MS Excel spreadsheet
  2. Tab-delimited Text File


Supplemental Table 4: Tumor samples from the Norway/Stanford data that were used calculate the expression centroids. In parentheses, the node correlation for the core samples included for each subtype.

Available as:

  1. MS Excel spreadsheet
  2. Tab-delimited Text File



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