how to classify a list of disease genes ?

Question

[Chaimaa]

Dear all,

I have a list of 200 to 300 disease genes, and I'm looking for a relevant and successfully used classification methods, which can be used and implement easily whether in Matlab or Python for classifying these disease genes.

Thanks

[Benn]

What exactly do you mean with classifying?

[Chaimaa]

classifying data into different classes according to some constrains.

[Chaimaa]

classifying genes into different classes according to some constrains.

[Benn]

That is more clear, thanks, you can use GO (gene ontology) to group your genes in functional categories. Or in your case you can try DOSE. I have never used it, but it sounds like it might be useful for you. Most of these tools are in R though.

[Chaimaa]

@ b.nota I'm looking for unsupervised classification methods

[Benn]

Yeah if your question is not clear, you can't expect clear answers either.

Usually people use clustering as unsupervised method, such as hierarchical clustering or k-means. Pretty straight forward in R, don't know about Matlab or Python.

[GenoMax]

Unless you specify the constraints along with nature of the input (just gene names?), how do you expect to get useful answers?

[Chaimaa]

@genomax, I want to apply classification to see if these genes, which i got by applying one regularization method are really significant or not! when i applied this regularization method, i got 200 to 300 genes and a coefficient measure along with them.

So; I really have only these gene's name list and no more information except their coefficient. and that's why i share with you guys to suggest me and help me out !!

[GenoMax]

So these genes are associated with a single "disease" i.e. they are not from different diseases? You do need to map them onto pathways to see if you have some genes that are significantly enriched. @EagleEye has mentioned one method below. You can also try Open Targets platform.

[Chaimaa]

yes they are associated with a single 'disease'.

[Chaimaa]

Actually i'm looking for unsuervised classification methods

Answer 1

[EagleEye]

You can perform functional/pathway enrichment analysis using your list of genes to check whether these genes are involved in the functions or pathways related to disease/cancer.

Here is the tool to perform this task, Gene Set Clustering based on Functional annotation (GeneSCF)

[Chaimaa]

@ EagleEyeI already applied DAVID to do pathway enrichment analysis, but i need to try so many cases and classification is the second case. hope you get what i mean Thanks.