Enrichment analysis

Scoring pathways association

During enrichment process the input gene set is compared to the pathways and processes from the reference database. A measure called XD-score is used to rank the pathways. XD-score uses a random walk to score how close a pathway and the input set are in the molecular interaction network. XD-score is relative to the background model. The score is equal to zero, if the input set -> pathway distance is equal to the average distance between the input set and all pathways. Positive values of XD-score indicate more significant relationship (see regression plot for XD-score significance threshold).

Pathways are listed in the results tab. A click on a pathway name will generate a view of the interaction network including the input gene set and the selected pathway.

Expanding pathways

At the same time, a pathway expansion is found using a human protein-protein interaction network. Only those proteins are added which are strongly associated with the pathway or which increase the pathway compactness by connecting its disconnected members.

Because pathway expansion is constructed using human protein interactions, for non-human gene sets the result might be meaningless (e.g. due to pathway rewiring in different organisms). Please interpret the results with care.

Steps of analysis

  1. select interaction network or upload your own
    (tab separated list of edges)
  2. select the identifier format of your gene set
  3. select a reference database of pathways and cellular processes
  4. optionally tick tissue specific XD-score calculation
  5. optionally set pathway expansion criteria in advanced options
  6. enter a list of genes/proteins and click "use gene list" button or select nodes from the current network view and click "use selected nodes" button
  7. click on a pathway name in the results tab to generate a network view