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Home | Search | Figures | Data | Info | Links | SGD | Microarray_Homepage 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 column. 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. Problems viewing images We recommend that you upgrade to the latest browser versions. For Netscape this is version 4.61 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;they do not however include links to the databases as the html versions of these figures do. 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 Gavin Sherlock.