Select Genes
============

![Select genes icon](icons/select-genes.png)

Manual selection of gene subset.

Signals
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**Inputs**:

- **Data**

  Data set.

- **Gene Subset**

  A subset of genes to be used for gene selection (optional).

**Outputs**:

- **Selected Data**

  A subset of genes selected in the widget.

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

**Select Genes** widget is used to manually create the gene subset. There are three ways to select genes:
- Manual gene selection (written input). The widget supports autocompletion for gene names.
- Selecting genes from gene sets in the "+" option.
- Selecting genes from a separate input (input can be adjusted in the widget).

![image](images/SelectGenes2-stamped.png)

1. Select *Gene Attribute* if there is more than one column with gene names.
2. Specify how you want to select your genes:
   *Select Genes from 'Gene Subset' input* adds genes from the separate input to selected genes.
   To create a new saved selection, click *Copy genes to saved
   subsets*. The genes will be listed in *Select Genes* text area below. To add these
   genes to an existing selection, click *Append genes to current saved selection*.
3. In *Select specified genes* you can type the gene name and the widget will automatically suggest corresponding
   genes. Genes that match the genes in 
   the input will be colored blue, while the unmatched will remain black.
4. The "+" button has a drop-down menu with two options.
   - *Import names from gene sets...* gives a list of gene sets and copies genes from selected sets into the list.
   - *Import names from text files...* imports gene names from the file.
5. *More* has two settings: *Complete on gene symbol names* (for easier
   gene selection) and *Translate all names to official symbol names* (for uniformity).
6. Set the organism to select the genes from (organism from the input data is chosen as default).
7. *Saved Selections* saves the most frequently used genes. "+" adds a new
   selection, "-" removes the existing one, and *Save* saves the current list. Double-click the selection to rename it.
8. *Output* for this widget is a data subset. If you wish to preserve the order of instances from
   your input data, tick the *Preserve input order* box. If *Auto commit is on*, all changes will
   be communicated automatically. Alternatively press *Commit*.

Below is a screenshot of the *Import Gene Set Names* option.

![image](images/SelectGenes4.png)

Example
-------

Below is a very simple workflow for this widget. We selected *AX4 Dictyostelium discoideum* data from
different time points and two different replicates from **PIPAx** widget. In **Select Genes**
we used the *Import names from gene sets...* option and selected two mRNA processes that gave us
a list of genes you can see in the *Select Genes* box. Then we fed these data into the **Data Table**.
There are 125 genes in the entire *AX4 Dictyostelium discoideum* data that are present in the
selected mRNA processes.

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