Correlation Engine Pathway

What is Correlation Engine pathway analysis?

Correlation Engine (CE) Pathway 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 pathway

Correlation Engine pathway 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 pathway

4. In the task set up page, select the right options for Organism, Data type, fill in the Project information and hit the Next button

1. Select at least one or more contrasts of interest for Correlation Engine pathway analysis

1. Click Finish to run

The result is stored under a Correlation engine 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

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.