comparison of expression profile between 2 groups

Question

[afzaljf911]

Dear All, How can I compare expression profile between 2 groups? I have TCGA somatic mutation and expression data. I have 2 groups as following: 1. samples with TP53 mutation 2. samples without TP53 mutation. I want to compare the expression pattern between these groups. I need a comprehensive, detailed and step by step workflow. Thanks,

Answer 1

[h.mon]

This is part of a long-running series called "google your own title". Spoiler: here are two answers:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570223/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516091/

(granted, I had to add tcga to the search terms.)

P.S.: as for detailed instructions, read edgeR and DESeq2 user guides, or look at the BioConductor workflows.

Answer 2

[Omics data mining]

Hello ,

For comparative mutation and expression data, you can use gitools available at http://www.gitools.org/home . Here, you can give input of multi dimesional data at a time and can get comprehensive results. You can find many tutorial for detail usage of this tool.