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- 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.
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