Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes

Josine L Min, George Nicholson, Ingileif Halgrimsdottir, Kristian Almstrup, Andreas Petri, Amy Barrett, Mary Travers, Nigel W Rayner, Reedik Mägi,
Fredrik H Pettersson, John Broxholme, Matt J Neville, Quin F Wills, Jane Cheeseman, the GIANT consortium, the MolPAGE consortium, Maxine Allen,
Chris C Holmes, Tim D Spector, Jan Fleckner, Mark I McCarthy, Fredrik Karpe, Cecilia M Lindgren and Krina T Zondervan

We provide data, code and a guide through the analysis for the readers of Min et al. (2011). For a detailed description of the data and the biological findings we refer the reader to the paper.


Data description and download

Coexpression network analysis

We provide the reader a guide through the analysis of coexpression networks related to metabolic syndrome. The data are gene expression profiles from the MolOBB study consisting of 44 healthy controls (27 men, 17 women) and 29 cases with Metabolic Syndrome (16 men, 13 women) collected from the Oxford Biobank as part of the MolPAGE consortium.

MolOBB gene expression data is available at ArrayExpress (E-MTAB-54).

Genotype data and Metabolic casecontrol status (EGAS00000000102) is available at EGA.


Characterizing and quantifying sources of variation of gene expression traits or module eigengenes

The MolTWIN dataset allowed us to decompose the biological and experimental variation underlying an expression trait into five components: familiality (genetic and common environment effects shared by twin pairs); individual environment (unique for twin individual); common visit and individual visit effects, which respectively measure the amount of shared (by twins within a pair) and non-shared variation occurring in the phenotype over the sampling period. The residual component of variation comprised experimental effects (two technical replicates of the same sample).

MolTWIN gene expression data is available at ArrayExpress (E-TABM-325).

Genotype data and Metabolic casecontrol status (EGAS00000000102) is available at EGA.


WGCNA tutorials

Rscripts are adjusted from the tutorials from the WGCNA website. The tutorials from the WGCNA illustrate installation instructions, step-by-step analysis of coexpression networks, the comparability and meta-analysis of multiple gene expression datasets as well as interfacing with VisANT software.


R Scripts