> For the complete documentation index, see [llms.txt](https://help.multiomics.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.multiomics.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/correlation-engine-pathways.md).
# Correlation Engine pathways
## What is Correlation Engine pathways analysis?
Correlation Engine (CE) Pathways analysis helps determine if your gene(s) of interest, identified by differential analysis in Connected Multiomics, corresponds to gene or protein sets from the GO consortium, MSigDB, TargetScan, and InterPro.
## Running Correlation Engine pathways
The **Correlation Engine pathways** task can be invoked on a differential analysis output data node. The filtered differential analysis output is recommended because it includes the genes of interest between comparisons.
1. Click a filtered feature list data node
2. Click the *Biological interpretation* section of the toolbox
3. Click *Correlation Engine pathways*
4. In the task set up page, select the right options for *Organism,* fill in the *Project information* and hit the *Next* button
5. Select at least one or more contrasts of interest for *Correlation Engine pathways* analysis
6. Click *Finish* to run
The result is stored under a *Correlation Engine* *pathways* node. To open it, double click on the node or select the respective Task report from the context sensitive menu.
## Task report
Use the dropdown list to switch between different contrasts. For each contrast, the report is a table with one pathway per row (*Gene set* column; the column entries are clickable for hyperlinks), with the category name in the *Title* column. The *Taxonomy* column tells the database sources, while the *Description* column provides more information about the pathway.
Illumina has developed the *Running Fisher* algorithm to perform pathway analysis in CE. See more details about the calculation of *Direction, Normalized enrichment score, Enrichment score*, and *P-value* in our technical note: [Data Correlation Details: Enrichment Analysis](https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote-data-correlation-enrichment.pdf)
## Visualizing Correlation Engine pathway results
Only if the report table has fewer than 100 pathways (rows), can they be visualized in the Data Viewer.
To make it easier to visualize, ICM includes the *“Open Data Viewer auto session”* link. By clicking it, a Data Viewer session will open with the top 30 pathways ranked by *Normalized enrichment score* for the contrast.
Two plots are loaded into the Data Viewer. Both plots show *Normalized enrichment score* on the horizontal axis and pathways (i.e. the ones present in the gene enrichment table) on the vertical axis. The plots show *Normalized enrichments scores* (*Normalized enrichment score* column of the task report table) and - in addition - the plot on the left uses color range to depict enrichment directions (blue = Up, red = Down).
To customize the content plotted, filter down the number of results. Type the value in the text box in the column header and hit enter (an example using a cut-off based on the *Normalize enrichment score is* shown below). Once the number of results falls below 100, the View plots in Data Viewer icon (*“Open Data Viewer custom session”*) will be displayed. Click the link to open a new Data Viewer session.
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