Gene Annotation Tool
Introduction
This web page provides an interface to query our database of keyphrases
for clusters of yeast or e-coli genes.
The keyphrases are drawn from MedLine abstracts related to the genes
and are chosen if they are representative of some significant portion
of the cluster.
Please contact us at the link below ("Links to us") with any comments
or suggestions you might have.
Instructions
The form to the right includes a number of fields:
- Gene names: type or paste in a list of names of genes,
separated by spaces and/or newlines. We have tried to compile a
broad list of possible aliases for genes so you should try the
identifiers you use first. If this does not work, try looking up
the gene in SGD (see the Useful related links below) and using
that name in your query.
- Maximum number of keyphrases: specifies a limit on the number
of keyphrases to be extracted.
- Only select 'significant' keyphrases: this field by default
is on, when set our code will only extract those keyphrases that
seem to be statistically significant (p < 0.05).
- Minimum number of keyphrases (despite significance): it is
possible when reporting only the significant keyphrases that you
may get only a small number or even just one keyphrase, this field
lets you set a minimum number of keyphrases to get no matter what
the probability associated with them is.
- Minimum total genes for keyphrase: the minimum number of
genes a keyphrase must be associated with to qualify as a
possibility.
- Minimum in cluster genes for keyphrase: the minimum number of
genes within the cluster a keyphrase must be associated with to
qualify (note, setting this value to anything greater than 1 may
greatly reduce your results).
Once you have filled in the form to your satisfaction press the Annotate
button.
The data values you have entered will be checked for obvious errors and
then the database consulted.
If one or more of the gene names you provide has a problem you will be
shown a window indicating these problems and asked to change your query.
Assuming your query makes it past all of the checks it will then enter our
database.
The resulting query will likely take at least four minutes to run and
perhaps up to 10 minutes, please do not press the stop in the window
that pops up during this process.
Useful related links
Links to us