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Supplemental Data 
Supplemental Table 1: Summary of clinicopathological information for the primary breast tumors used in the array CGH analysis. The total number of genomic aberrations (gains plus losses) is derived from supplemental Tables 2 and 3.
Available as:
  1. MS Excel spreadsheet
  2. Tab-delimited Text File

Supplemental Figure 5: Measuring X-chromosomal DNA copy number variation.
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  1. HTML Document
  2. Portable Document Format

Supplemental Information: Estimating the significance of altered fluorescence ratios.
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  1. HTML Document

Supplemental Table 2: Summary of DNA copy number gains identified in breast cancer cell lines and primary breast tumors. DNA gains are indicated ("X") if the corresponding chromosomal arm contains more than one statistically significant increased fluorescence ratio (as defined above in "Estimating the significance of altered fluorescence ratios"), specifying a false discovery rate of 1%.
Available as:
  1. MS Excel spreadsheet
  2. Tab-delimited Text File

Supplemental Table 3: Summary of DNA copy number losses identified in breast cancer cell lines and primary breast tumors. DNA losses are indicated ("X") if the corresponding chromosomal arm contains more than one statistically significant decreased fluorescence ratio (as defined above in "Estimating the significance of altered fluorescence ratios"), specifying a false discovery rate of 1%.
Available as:
  1. MS Excel spreadsheet
  2. Tab-delimited Text File

Supplemental Table 4: Correlations between total numbers of genomic aberrations (gains plus losses) and clinicopathological features of breast tumors (see supplemental Table 1). Statistically significant associations (Student's T test, 2-tailed) are indicated.
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  1. Portable Document Format

Supplemental Information: Additional content referring to published Figure 2.
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  1. HTML Document

Supplemental Figure 6: DNA copy number alteration across chromosome 17 by array CGH.
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  1. HTML Document
  2. Portable Document Format

Supplemental Information: Additional content referring to Supplemental Figure 6.
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  1. HTML Document

Supplemental Figure 7: DNA copy number alteration across chromosome 20 by array CGH.
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  2. Portable Document Format

Supplemental Table 5: Highly-amplified genes displaying moderately or highly elevated mRNA levels. The 54 genes display moderately- (fluorescence ratio >2) or highly-elevated (ratio>4) mRNA levels when highly-amplified (ratio>4) in one or more breast cancer cell line or tumor samples. In total, this list includes gene amplifications from 3 different breast cancer cell lines and 11 different primary breast tumors, encompassing 22 different cytobands. Known oncogenes are identified. Candidate oncogenes (noted) have been proposed based primarily on cytogenetic locations, high expression levels, and/or plausible functional roles.
Available as:
  1. MS Excel spreadsheet
  2. Tab-delimited Text File

Supplemental Information: Details of the linear regression model used to estimate the fraction of variation in gene expression attributable to underlying DNA copy number alteration.
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  1. HTML Document

Supplemental Figure 8: DNA copy number profiles are provided for a representative set of breast cancer cell lines and tumors (listed below). For each cell line/tumor included, two representations are shown. The first representation displays moving average (symmetric 5-nearest neighbors) ratios on a log10 scale, with genes mapped by nucleotide position. Green indicates fluorescence ratios <0, and red indicates fluorescence ratios >0. The second representation (labeled 'b') displays the graphical output of the statistical method (see Supplemental Information: Estimating the significance of altered fluorescence ratios, above) used to identify chromosomal gains/losses. Here, ratios are plotted on a log2 scale, and black tick marks indicate fluorescence ratios estimated to be significantly different from baseline normal vs normal hybridizations (see "Estimating significance of altered fluorescence ratios, above), specifying a false discovery rate of 1%.
Available as Portable Document Format only:
  1. 46,XX
  2. 46,XX (b)
  3. 47,XXX
  4. 47,XXX (b)
  5. BT474
  6. BT474 (b)
  7. MCF7
  8. MCF7 (b)
  9. T47D
  10. T47D (b)
  11. Norway 12
  12. Norway 12 (b)
  13. Norway 39
  14. Norway 39 (b)
  15. Norway 48
  16. Norway 48 (b)
  17. Norway 57
  18. Norway 57 (b)
  19. Norway 109
  20. Norway 109 (b)
  21. Norway 111
  22. Norway 111 (b)
  23. Stanford 31
  24. Stanford 31 (b)

Supplemental References:
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