Constructing PPI, GGI, and Coexpression Networks from TCGA Data

[Sandhya]

Good After Noon All,

I'm seeking guidance on constructing Protein-Protein Interaction (PPI), Gene-Gene Interaction (GGI), and Coexpression networks using TCGA data from UCSC Xena and Cancer Genomics Browser. Specifically, I'm interested in extracting genes from TCGA data and mapping them to databases like String or Biogrid for PPI and GGI analysis. Additionally, I aim to include all protein interactions related to proteins in the database. Could anyone provide insights or suggestions on how to approach this?

Thank you in advance for your help!

[Mary Goldman]

Hi Sandhya,

I'm afraid we're not funded to advise on how to extract PPI, GGI, and coexpression networks but you may find it useful to download our data to work with: https://xenabrowser.net/datapages/. We have both gene expression (GDC and legacy TCGA) and protein expression (legacy TCGA only). Let me know if there's other data you're interested in!

Others on the mailing list may comment on how they have built these!

Best,

Mary

-----

Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

--
You received this message because you are subscribed to the Google Groups "UCSC Xena and Cancer Genomics Browser" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ucsc-cancer-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/ucsc-cancer-genomics-browser/342ce8a2-5376-4246-b547-f92ba78822d9n%40googlegroups.com.