Gene Expression Downstream Analysis

Question

[always_learning]

Hi,

I did Survival Analysis on a Group of genes using TCGA( Thanks to Biostar) and found that some of them have very significant role based on P Values in some Cancers. Now I just wanted to relate these Genes with some other genes very relevant for some important pathways, although my studied genes are not directly part of these pathways. basically, I just wanted to see that if the expression of these genes has anything to do with ( up regulation and down regulation ) with a particular set of gene(s) Since I am pretty new to such sort of analysis then can some guide me what sort of things I could do for such cases.

Thanks

[BioinfGuru]

2017 Paper with an R package relevant to this type of analysis:

Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.

Answer 1

[theobroma22]

Since you are working with human tissues, you have the EntrezIDs. Check out the SPIA package available on the Bioconductor website.

Answer 2

[always_learning]

Thanks !! Is there any other tools or method or tutorials apart from this as well?

Thanks Najeeb