WGCNA analysis of microarray data from H0351.2001

Science
1

Hi,

I found this WGCNA analysis of microarray data from one person H0351.2001
http://api.brain-map.org/examples/wgcna/index.html

I am wondering how representative the analysis is and if there is any chance to integrate microarray expression values of all 6 available persons from ABA (H0351.2001, H0351.2002, H0351.1009, H0351.1012, H0351.1015, H0351.1016)?

Does anyone have experience with such kind of analysis or knows a workflow or code in R or Python?

Thank you for your help!

2

Hi @Libra66. I’m glad to see you are interested in this analysis. The short answer is that (1) this is very representative of values across all six donors (see below), and (2) I’d encourage you to explore the tutorials on the WGCNA R package site.

We’ve actually published two papers looking at this very question! The first was our initial publication on the Allen Human Brain Atlas (Hawrylycz, Lein et al 2012), where we performed the WGCNA analysis at your example above on the first two brains, and found modules corresponding to several brain regions and broad cell types. In the second paper (Hawrylycz, Miller, Menon, et al 2015) we repeated this analysis on all six brains, and identified 32 modules, characterizing what they represent and how conserved they are across brains (quite conserved!). There is quite a bit more included in these papers as well, and feel free to post any additional questions you have here! I could also probably dig up the scripts from these papers if you’d like.

3

Dear jeremyinseattle,

thank you very much for this worthwhile information! It helps us really a lot for our project.

In case of additional questions, indeed, I would contact you again.

All the best,

Libra66