Cell Cycle Analysis Home
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cell cycle project
This page contains information on on how to
use this site.
- How do I find out if a gene is cell cycle regulated?
The easiest way to determine if a gene mRNA level is cell cycle regulated (and
when its expression peaks) is by using the search feature. If a gene
is cell cycle regulated when it peaks will be indicated in the peak
- How do I interpret those funky looking red and green images?
The data for one gene corresponds to one row, and the time points of each experiment
are the columns. 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 2.8 to 1.
Ratios greater than 2.8 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.
- What is the 'Score'?
The score is a number that we generated alogorithmically as an indication
of how well the data for a gene indicated that the gene was cell cycle regulated.
The details of this calculation are presented in our
paper, but simply stated, the higher the score, the better the expression data
indicated that the gene is cell cycle regulated.
- Why are the graphs plotted as log(ratios)?
If we plotted absolute ratios, then 2-fold induced would be plotted as 2,
and 2-fold repressed would be plotted as 0.5, which would not make sense.
Hence we take logs (in base 2), such that a 2 fold increase is plotted
as 1, and a two-fold decrease is plotted as -1. Taking logs therefore
introduces a symmetry around zero for induced vs repressed genes, such
that inductions or repressions of equal magnitude are numerically
equal but of opposite sign.
- So how are the peak to trough ratios calculated?
These are calulated from the absolute ratio values, that is the highest ratio,
divided by the lowest. If there are zero, or one data points for a gene in a
particular experiment, then the idea of a peak to trough ratio is not applicable.
- Why do some genes return more 'similar genes' than others?
We calculated similarity scores using a correlation algorithm, and only consider as significant
those correlation scores above 0.5. One gene may have many more significantly similar genes than
another. Further we only generated similarity scores between the top 1200 most periodic
genes, as similarities between genes whose levels fluctuate minimally
are meaningless. Please note that the similarity measure between
expression profiles that we use here is not as sophisticated as the
one used in our paper. They will give similar, but not identical, results.
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- Where can I find descriptions of the experiments?
Full descriptions of all materials and methods are published in the paper.
- If you still have a question that is not answerered here please
email Paul Spellman or