Information on how to use this site

1. How to search the dataset ?
2. Cross hybridization notice
3. Problems viewing figures
   
4. What database system are you using ?
   
5. If you still have a question that is not answered...

You can search for a string in the name column or in the ORF column. The program will look for any record containing this string. For exemple, if you submit the query "gene containing: dr", you will obtain DRS2, PDR3, ADR1, PDR15, PDR1, ...
Some tips:
    - the search is case insensitive
    - the ratios are shown visually by the classical color code: red = induction, green = repression.

You can order the result by name, gene, or ratio with the "order by" button
    - informations on gene process and function from the last version of SGD orf description file (june 23 2001)

One of the challenges in measuring mRNA levels on microarrays is that genes can cross-hybridize, depending on whether the probes target unique or common regions. In order to predict these events and find unique regions, all S. cerevisiae ORFs were BLASTed against all others, with E=1E-5, gaps enabled and low-complexity filtering disabled. The shortest resulting hits were 24/24. Matches to self and to the wrong strand (i.e., not transcribed) were not considered. A minimum of 50 bases was required for unique regions. This has been done by Adnan Derti and the corresponding files can be found at Church Lab .

Three levels of cross hyb have been defined:

: no problem
: some xhyb but some unique regions (max unique region>=50 bases)
: small or no unique regions (max unique region<50 bases)

This is only provided as information, cross hybridization can occur even if you can find some specific regions.

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