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This website contains the complete data sets for the experiments in the paper - DeRisi et. al. Science 278: 680-686, as well as the images of the whole-genome microarrays. The data is available for searching over the web and also as text files that can be downloaded. Please bear in mind that this site, including the help page, is constantly being updated and improved. We welcome all suggestions.

Beginning searches
The search page for each of the databases allows you to query the database by ORF name, Gene name or Description (as obtained from the Saccharomyces Genome Database - SGD). You will need to use the 'contains' option for wild-card searches if you don't type in the exact name. These fields are case-insensitive. You can use the array coordinates (see Additional figures and information) to search for specific spots on the microarray. Use the 'Start search' button at the bottom instead of the return key.

You can also search for genes with specified induction or repression ratios (for the metabolic time-course, at each of the different time-points during the growth curve). Note that you have to type in a number less than 1 for genes that are repressed relative to the reference. Searches can be combined using the 'AND' or 'OR' operators at the bottom. For instance on the metabolic time-course search page, a search for genes whose 'Description' 'contains' 'ribosomal' AND whose 'Fold increase at O.D. 6.9' is 'less than' 0.3, yields 20 ribosomal protein genes that are strongly down-regulated at the diauxic shift. Search results may be sorted for display using the options at the bottom.

Search results
A maximum of 25 genes meeting the search criteria are displayed per page. Additional results can be viewed using the appropriate links. In the metabolic time-course database, black diamonds indicate no significant differential expression (less than 2-fold) at the indicated time-point (1 through 7) relative to the first, whereas red or green arrows indicate induction or down-regulation by a factor of more than 2. Entries in the TUP1 and YAP1 databases are self-explanatory.

The row number in the metabolic time-course database is a link to more extensive data about the gene during the experiment. This page also has a link to the SGD entry for the gene. These are yet to be implemented in the other databases.

Additional figures and downloading data
Follow this link on the homepage to see complete images of the whole-genome microarrays, some of the figures in the paper and download the data as a text file. Save the 'Download...' link to a file on your computer to obtain all the data as a tab-delimited text file. Spots on the microarray images are defined by their array coordinates. Each microarray is divided into 4 quadrants and the coordinates for a spot is x,y,z where x is the quadrant number, y is it's position along a row in that quadrant, and z is it's position down a column in that quadrant.

Comments? e-mail jderisi@cmgm.stanford.edu or vishy@cmgm.stanford.edu
Last modified 11/6