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 😉

The Network of Cancer Genes database

In the last year I have been part of the team maintaining and updating the Network of Cancer Genes database, also known as NCG.

NCG logo
The Network of Cancer Genes database

The main focus of NCG is to provide a curated list of genes associated to cancer, obtained after a manual review of the literature, and classified by cancer subtypes. Moreover NCG annotates some system-level properties of genes associated to cancer, from their protein interactions to their evolutionary age, and from the presence of paralogs in the human genome to their function.

NCG is a small database and is not supported by any big consortium, but we do our best to fill our niche :-). The following list will describe you what you can get from NCG and how can it be useful to you.

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