How to do subtype assignment for expression data

Question

[berry]

Hi,

I'm working with RNA-seq data of GBM (Glioblastoma) samples (tumor only). I want to see which subtype my samples are belong to, based on a previous study which divides GBM into 3 subtypes. Each of these subtypes has 50 signature gene list.

What would be the best way of assigning my samples to these subtypes?

Many thanks!

Answer 1

[Kevin Blighe]

Hello,

You will have to create a predictive model of the GBM sub-types using the '50 signature gene list', and then use this model to predict the sub-types in new data.

Kevin

[berry]

Thanks Kevin!

Just to note here for the people who work on GBM, I found this portal to assign expression data to 3 GBM subtypes (Wang et al 2017): http://gliovis.bioinfo.cnio.es/