KEGG Pathways
=============

Diagrams of molecular interactions, reactions, and relations.

**Inputs**
- Data: Data set.
- Reference: Referential data set.

**Outputs**
- Selected Data: Data subset.
- Unselected Data: Remaining data.


**KEGG Pathways** widget displays diagrams of molecular interactions,
reactions and relations from the [KEGG Pathways
Database](http://www.genome.jp/kegg/pathway.html). It takes data on gene
expression as an input, matches the genes to the biological processes
and displays a list of corresponding pathways. To explore the pathway,
the user can click on any process from the list or arrange them by
P-value to get the most relevant processes at the top.

![](images/kegg_pathways/KEGG-Pathways-stamped.png)

1.  Information on the input genes.
2.  If you have a separate reference set in the input, tick *From
    signal* to use these data as reference.
3.  To have pathways listed and displayed by vertical descent, tick
    *Show pathways in full orthology*.
4.  To fit the image to screen, tick *Resize to fit*. Untick the box if
    you wish to explore the pathways.
5.  To clear all locally cached KEGG data, press *Clear cache*.
6.  When *Auto commit is on*, the widget will automatically apply the
    changes. Alternatively press *Commit*.
7.  A list of pathways either as processes or in full orthology. Click
    on the process to display the pathway. You can sort the data by
    P-value to get the most relevant results at the top.

Example
-------

This simple example shows how to visualize interactions with **KEGG Pathways**. We have loaded the *Caffeine effect: time courses and dose response* (GDS2914) data with the **GEO Data Sets** widget. Then we have observed the pathways in **KEGG Pathways**. We have used reference from signal and selected *AGE-RAGE signaling pathway in diabetic complications*.

![](images/kegg_pathways/KEGG-Pathways-Example.png)