Pathway analysis using the GSEA workbench in Qlucore Omics Explorer


Gene Set Enrichment Analysis (GSEA) is a widespread method to analyze datasets using functional information such as pathways, gene sets and other structured lists of biologically relevant information.

Qlucore Omics Explorer has implemented the GSEA method in a generic, fast and easy to use workbench, ideal for biologists that want to perform pathway analysis or identify other lists that can explain structures in an experiment.

First you load a dataset in Qlucore, start the workbench and select relevant functional information, like pathway files from public repositories. It is also possible to work with your own compiled gene lists in text files.

Next, the ranking criteria is selected. This is done the same manner as in the Statistics window. As an example, the GSEA workbench can rank the pathways based on differences between two biological groups, using a t-test. The workbench ranks all selected pathways based on the calculated Enrichment Score for each pathway. Corresponding p and q values are also calculated. With only one keypress the relevant pathway list(s) can be transferred to a variable input list in Qlucore Omics Explorer and be used for further analysis.

Gene set definitions are often acquired from open online repositories, one such example is MSigDB from Broad Institute.

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