What Are The Most Useful Pathway Databases For The Analysis Of Genes Mutated In Cancer?

Question

[Christian]

I'd like to compile an up-to-date list of pathway databases that are most useful for analyzing lists of genes mutated in cancer. The focus on cancer demands high-quality signaling pathways, but the database should not be limited to those.

I know that similar questions about pathway databases and analyses have been asked before, but they were not specific about the requirement to analyze cancer genomes.

Currently, I am aware of the following resources (which I also use):

• NCI Pathway Interaction Database (no longer updated since 2012)
• WikiPathways
• KEGG
• REACTOME
• BioCarta
• BBID

My impression is that the NCI Pathway Interaction Database is most useful in this context, but it is no longer maintained. WikiPathways made also a good impression on me in terms of quality and coverage.

Is there any important pathway database I miss? What databases do you use for pathway analysis of genes mutated in cancer?

Answer 1

[Giovanni M Dall'Olio]

Are you interested only in the databases that annotate pathways, or in any database that can be used to determine the impact of a mutation observed in cancer?

Some other tools for the pathway analysis:

• STRING Computational prediction of protein interactions, assembling predictions from multiple sources.
• UNIPROT Pathways not very well known, but contains some well annotated pathways.
• BIOCARTA Pathways nice drawings of pathways.
• GSEA / MSigDB (for mouse)

[zx8754]

GeneMANIA. Also, some tutorials: http://bioinformatics.ca/workshops/2012/pathway-and-network-analysis-omics-data

[Christian]

I am only interested in annotated pathways for pathway analysis, not in mutation effect prediction.