CODEWITHSUNDEEP
cluster-analysisbioinformaticspcagenetics
bioman
bioman

Reputation: 1

Cluster gene expression to specific breast cancer subtypes in R using clinical parameters and gene expression data

I have a set of gene expression values of 1500 genes from breast cancer samples of 3 different subtypes and their clinical parameters. I need to cluster the gene-expression based on the breast cancer subtypes to find unique genes to each of the breast cancer subtypes. I had tried PCA and Kmeans but couldn't explain the name of subtypes. Is there any method to do this? Thanks in Advance.

Upvotes: 0

Views: 74

Answers (1)

rajsuryan
rajsuryan

Reputation: 171

What you're looking for are differentially expressed genes. If you have expression data for the three subtypes, you can use a differential expression analysis tool (DESeq2 and EdgeR are commonly used) to get the genes that are differentially expressed among your samples. The analysis gives you the extent of differential expression as well as the statistical confidence of the results.

If you also have a control sample, you can infer genes that are specifically up or down-regulated in a certain subtype from the list DEGs.

This is a helpful reference to learn more about the theory as well as the application of differential expression analysis - Introduction to DGE

Upvotes: 0

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