Called Pathways Result

The result of a Identify Pathways run is very similar to the pathway database, see The Pathway Database, in that it has three views:

Note that the latter two are identical to the views in the pathway database, except that the pathways opened from these views are enriched with the data from (differential) abundance tables, see below.

The Identified Pathways Table

The result of a Identify Pathways run presented as a table where each row corresponds to a pathway with a pathway name, pathway id and for each sample or comparison, depending on whether an abundance table or a differential abundance table has been used, a number of statistics on the pathway call (figure 14.22).

Image identify_pathways_result1
Figure 14.22: The result of the Identify Pathways tool is a table with pathways in the rows and some columns describing the pathway calls for each sample or comparison. Here the result is shown for a differential abundance table.

There are two general columns to describe the pathways that have been called.

For each sample or comparison, there are four columns summarizing the result of the pathway calling procedure. Note that empty fields in this table mean that a pathway is not part of any solution for a given sample or comparison.

Depending on whether the input has been an abundance table or a differential abundance table, the result may contain some more columns giving average statistics for the EC terms from the (differential) abundance table for the whole pathway in which they occur. For an abundance table the column Average abundance gives the average abundance for all identified (not-filtered) EC terms that are present in the pathway. Similarly, for a differential abundance table the metrics are summarized by averaging over all identified (not-filtered) EC terms in a pathway, specifically the Average max group mean and Average fold change are reported.