GenExpress
==========

![Widget icon](icons/genexpress.png)

Gives access to [**GenExpress**](https://www.genialis.com/genexpress/) databases.

Signals
-------

**Inputs**:

- (None)

**Outputs**:

- **Data**

  Selected experiments. Each annotated column contains results
  of a single experiment or, if the corresponding option is
  chosen, the average of multiple replicates.

Description
-----------

**GenExpress** is a widget for a direct access to [**GenExpress**](https://www.genialis.com/genexpress/)
database. It is very similar to the **PIPAx** and **GEO Data Sets** widgets as it allows you 
to download the data from selected experiments.

![GenExpress widget](images/GenExpress-stamped.png)

1. Choose a projects to source your data from.
2. Use *Selection bookmarks* to save a selection: select experiments, click the "**+**" button 
   and name the set. To add experiments to your set, click on the set name, select additional 
   experiments and click *Update*. To remove the set click "**-**".
3. In *Sort output columns* set the attributes by which the output columns are sorted. Add 
   attributes with a "+" button and remove them with "-". Switch the sorting order with arrows on the right.
4. Set the expression type for your output data.
   - **Expression RPKM** outputs data in *reads per kilobase of transcript per million mapped reads*
   - **Expression RPKUM** outputs only RPKUM data.
   - **Read counts (raw)** outputs raw read count data. <br>The polyA variants use only polyA (mRNA) mapped hits.
5. **Exclude labels with constant values** removes labels that are the same for all selected experiments.<br>
   **Average replicates (use median)** averages identical experiments by using medians as values.<br>
   **Logarithmic (base 2) transformation** returns log<sub>2</sub>(value+1) for each value.
6. Click *Commit* to output selected data.
7. Select the server you wish to access the data from. Log in to access private data.
8. *Clear cache* removes the uploaded data sets from internal memory.
9. Experiments can be filtered with the *Search* box. To select which attributes to display right-click 
   on the header. To select multiple experiments click them while holding the *Control/Command* key.

Example
-------

In the schema below we connected **GenExpress** to **Data Table** to view the gene expression reads
and then to **Scatter Plot**, where we chose to view expression levels from two experiments. In the plot
we select an outlier and view it in another **Data Table**.

![](images/GenExpress-Example.png)