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"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.

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The tool is simple to use:
  • STEP 1: Select the data compendium through which the Signature tool should search.

    step 3

  • 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 1

  • STEP 3: select microarray probe(sets) for each gene.

    step 2

  • 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.

Now, 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 Professional).

Start using
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