NCG enrichment implemented in DOSE

I would like to give a big thanks to Guangchuang Yu, the author of many cool R libraries like GoSemSim and ggtree, for implementing a Network of Cancer Genes enrichment function in the DOSE R library.

The new function is called enrichNCG, and can be found in the github version of DOSE. You can use it to analyze a list of genes, and determine if they are enriched in genes known to be mutated in a given cancer type. For example, a random list composed by genes having an Entrez Id between 4000 and 9000 is enriched in genes mutated in sarcoma and leukemia:

If you have multiple sets of genes, you can also use the clusterProfiler library to compare them at the same time. Read this previous post for more examples of this functionality.

If you also have gene scores (e.g. a value for the expression or conservation of each gene), you can do a Gene Set Enrichment Analysis, which will give more importance to genes with higher scores:

You can also produce many nice plots. For example this is a cnetplot, in which each gene is connected to the terms related to it:

It is worth to mention that the DOSE package allows to calculate enrichment in the Disease Ontology database, which associates genes to disease terms. In my experience, for bioinformaticians Disease Ontology is more useful than OMIM, because it provides a clear association between genes and disease terms. If you use the raw OMIM data instead, you will have to text mine the descriptions and that can lead to a lot of noisy data.

Have a good enrichment with DOSE and NCG 😉