Home
Takes you to the Breast Cancer Microarray Hompage 

Figures
Enhanced figures from the paper plus web supplements 

Search
Search the Breast Cancer Microarray dataset 

Paper
Get a reprint in PDF format 

Data Download Get the raw data 

Weblinks and Protocols
Selected informational websites 

Help
Help for interpretation of the data 

People
Individuals and Institutions involved in the Breast Cancer Microarray Project  
 



  • How do I interpret the red and green images?
    The data for one gene corresponds to one row, and each experiment is represented by a column. The ratio of induction/repression is such that the magnitude is indicated by the intensity of the colors displayed. If the color is black then the ratio of control to experimental cDNA is equal to 1, while the brightest colors (red and green) represent a ratio of 8 to 1. Ratios greater than 8 are displayed as the brightest color. In all cases red indicates an increase in mRNA abundance while green indicates a decrease in abundance in the experimental sample with respect to the control. Gray areas (when visible) indicate absent data, or data of low quality.





  • How is the similarity between two genes determined?

  • The similarity of two genes in expression space is determined by calculating a distance measure across all experimental values. For this we are using two different formulas, the Pearson correlation or Euclidian distance (see below).

  • What is the difference between Euclidian distance and Pearson correlation?

  • In general terms, by computing the Pearson correlation, we compare the shape of the curves described by two genes expression values. The resulting value is the Pearson correlation coefficient.

    The Euclidian distance measure will compare the shape and the amplitude of the expression curves. This way, visually more similar genes will line up next to each other.

    To experience the difference between these two ways of calculating gene similarity, use the search function with different settings. If you look carefully, you can see the effect.

  • Problems viewing images
    We recommend that you upgrade to the latest browser versions. For Netscape this is version 4.51 for PowerPC Macintoshes, and Windows95/98 PCs. For 68K Macintoshes, and Windows 3.1 PCs you should get Netscape version 4.08. If you use Internet Explorer you should use version 4.5 on a Mac, and version 5.0 on a PC. If you still have problems then it may be that your computer doesn't have enough memory, or a fast enough processor. There are PDF versions of all figures which are somewhat less resource intensive.


| Home | Figures | Search | Paper | Data | Weblinks | Help | People |