how to classify a list of disease genes ?
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4.1 years ago
Chaimaa ▴ 250

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

genes classsification matlab python • 1.2k views
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What exactly do you mean with classifying?

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classifying data into different classes according to some constrains.

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classifying genes into different classes according to some constrains.

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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.

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

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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.

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

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@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 !!

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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.

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yes they are associated with a single 'disease'.

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Actually i'm looking for unsuervised classification methods

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4.1 years ago
EagleEye 7.0k

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)

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@ 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.