How to find genes that are involved in particular pathway?

Question

[arta]

Hi,

I have list of genes and I want to know whether these genes are involved particular pathway? For example I have 1000 genes, lets say 20 genes are involved in a specific pathway, like that.

I have to do that in Python.

I will be glad if you help me

[russhh]

which set of pathway definitions do you want to consider and which species are you working with?

[arta]

I am working with human cancer data sets, for pathways there is no restriction but obviously mostly about cancer.

[NB]

I am not sure if there is a better way but since your interested in cancer genes in particular, maybe you can have a look at NetAge.. Download the genes involved in your pathways of interest and overlay it with your gene list... or you could even have a look at PANTHER

[arta]

Thank you so much I will check them out...

Answer 1

[GouthamAtla]

You can always search the genes against wikipathways using wikipathways Api in perl,Python or Java. in a loop , you can retrieve all the pathways the given lost of genes are involved. You have the flexibility to search by specific terms like "cancer", "diabetes" etc.

Answer 2

[emekdemir]

If you have the uniprot identifiers try this PathwayCommons webservice

If you play with the url you will find out that there are plethora of information you can reach via PC webservices. The data is coming from Reactome, NCI-PID, Panther, BioCyc and others.

More info on http://www.pathwaycommons.org/pc2/

Ask more questions if you need more help.

Best,
ED

Answer 3

[EagleEye]

Try this, if you deal with human genes: Gene Set Clustering based on Functional annotation (GeneSCF)

Answer 4

[masspeclj]

I assume Wikipathways also allows searching for a specific protein (http://vocabularies.wikipathways.org/wp#_data_properties lists wp:Protein as a class) but there is not an example of SPARQL search for proteins on the query example page. Would someone please help me construct a valid SPARQL query for a specific protein?

Duane