YeastSpec (an acronym for "Yeast Specification") inputs a list of yeast gene names, and outputs a summary of functional classes, cellular localizations, protein complexes, etc. that are enriched in the list. The classes and categories evaluated were downloaded from the MIPS Database and the GO Database indicated below last downloaded on June 22, 2005. In addition, many published datasets have been compiled to evaluate enrichment against. Hypertext links to the publications are given.
The p-values, calculated using the hypergeometric
distribution, represent the probability that the intersection of given list with any
given functional category occurs by chance. The Bonferroni-correction divides
the p-value threshold that would be deemed significant for an individual test, by the
number of tests conducted and thus accounts for spurious significance due to multiple
testing over the categories of a database. After the Bonferroni correction, only those
categories are displayed for which the chance probability of enrichment is lower than:
p-value/#CD where #CD is the number of categories in the selected database. Without the
Bonferroni Correction, all categories are displayed for which the same probability of
enrichment is lower than: p-value threshold in an individual test
Note that
many genes are contained in many categories, especially in the MIPS database (which are
hierarchical) and that this can create biases for which YeastSpec currently
makes no compensation. Also the databases are treated as independent from one another,
which are really not the case, and each is searched separately, which may not be optimal
for statistical calculations. Nonetheless, we find it useful for sifting through the
results of clustering analysis, TAP pull downs, etc.
For more information, click
here.
The raw text files containing the annotation information and underlying database files can be downloaded here.
