Question: What Are The Most Useful Pathway Databases For The Analysis Of Genes Mutated In Cancer?
5
gravatar for Christian
6.0 years ago by
Christian2.8k
Cambridge, US
Christian2.8k wrote:

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):

My impression is that the NCI Pathway Interaction Database is most useful in this context, but it is no longer maintained.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?

pathway database cancer • 2.4k views
ADD COMMENTlink modified 6.0 years ago by Giovanni M Dall'Olio26k • written 6.0 years ago by Christian2.8k
1
gravatar for Giovanni M Dall'Olio
6.0 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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:

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Giovanni M Dall'Olio26k

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

ADD REPLYlink written 6.0 years ago by zx87547.9k

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

ADD REPLYlink written 6.0 years ago by Christian2.8k
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