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.
What exactly do you mean with classifying?
classifying data into different classes according to some constrains.
classifying genes into different classes according to some constrains.
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.
@ b.nota I'm looking for unsupervised classification methods
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.
Unless you specify the constraints along with nature of the input (just gene names?), how do you expect to get useful answers?
@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 !!
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.
yes they are associated with a single 'disease'.
Actually i'm looking for unsuervised classification methods
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)
@ 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
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