"Who else has found similar results?"
"Which drugs cause a similar expression signature?"
"In which cell lines does this signature occur?"
These are typical questions that can be answered
using the Signature tool.
The tool is simple to use:
- STEP 1: Select the data compendium through which the Signature
tool should search.
- STEP 2: Enter a list of genes (minimum 8) and the
corresponding expression values (absolute or relative)
which you have obtained from your own experiment (e.g. from
RT-qPCR, microarray, or RNA-seq).
- STEP 3: select microarray probe(sets) for each
- STEP 4: click on "Run" in the Signature tool.
That's it! GENEVESTIGATOR will use your signature as a
template and search for the most similar expression profiles
across the conditions available in the chosen sample
selection. Switch to another microarray platform to work with
an independent set of conditions.
there are a couple of things to have in mind:
- The signature tool works with log-scaled
data. If you have entered linear-scaled data, it will
log-transform it prior to the analysis.
- Two types of expression profiles exist in
GENEVESTIGATOR, absolute and relative. Absolute
values are used in the profiles for the Samples, Anatomy
and Cancers tools. In contrast, the Perturbations
profiles consist of relative values (experimental
versus control). Therefore, if you enter a signature
consisting of (log)-ratios of treatment versus control
samples, you are working with relative values and will be
able to choose only the Perturbations profiles. On the
other hand, if you entered absolute expression values, you
will be able to search either against the Samples, Anatomy
or Cancers profiles.
- Different distance measures can be used to
calculate similarities between your expression vector and
expression data from the database. None of them is a
priori more suitable for this tool, so try them out and
look at the results.
- Once you have obtained results, you can export
either the image or the data behind your figure using the
"Results" menu (available only for subscribers of